I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 6 10:15:17 -12 2024 I: pbuilder-time-stamp: 1704579317 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pyranges_0.0.111+ds-4.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 14 20:33:17 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-4.dsc: no acceptable signature found dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3880/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='572316125f1f4d25ab21316b053f01d7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3880' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4GivT2UO/pbuilderrc_yG9o --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4GivT2UO/b1 --logfile b1/build.log pyranges_0.0.111+ds-4.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux cbxi4pro0 6.1.0-17-armmp #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Apr 23 2023 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 2023 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 2022 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 2023 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 2023 more -rwsr-xr-x 1 root root 38496 Mar 23 2023 mount -rwxr-xr-x 1 root root 9824 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 14152 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 2023 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 2023 tar -rwxr-xr-x 1 root root 9800 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 2023 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3880/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17881 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bsdextrautils{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts3{a} libhtscodecs2{a} libicu72{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-dateutil{a} python3-distutils{a} python3-execnet{a} python3-hypothesis{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-setuptools{a} python3-six{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-tz{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-dev python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 43.0 MB of archives. After unpacking 190 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf tzdata all 2023c-5+deb12u1 [296 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf bedtools armhf 2.30.0+dfsg-3 [567 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf cython3 armhf 0.29.32-2+b1 [1230 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 35 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.3~deb12u1 [591 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf python3-distutils all 3.11.2-3 [131 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf dh-python all 5.20230130+deb12u1 [104 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1+deb12u1 [62.1 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-10+deb12u4 [346 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libncurses6 armhf 6.4-4 [81.1 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf python3-all armhf 3.11.2-1+b1 [1060 B] Get: 65 http://deb.debian.org/debian bookworm/main armhf python3-attr all 22.2.0-1 [65.4 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf python3-six all 1.16.0-4 [17.5 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf python3-dateutil all 2.8.2-2 [78.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf python3-execnet all 1.9.0-1 [41.5 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf python3-hypothesis all 6.67.1-1 [270 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 72 http://deb.debian.org/debian bookworm/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf python3-natsort all 8.0.2-2 [39.0 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf python3-pkg-resources all 66.1.1-1 [296 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf python3-numpy armhf 1:1.24.2-1 [4165 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf python3-ncls armhf 0.0.63-hotfix+ds-1+b3 [309 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf python3-packaging all 23.0-1 [32.5 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf python3-tz all 2022.7.1-4 [30.1 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf python3-pandas-lib armhf 1.5.3+dfsg-2 [3167 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf python3-py all 1.11.0-1 [89.2 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf python3-tabulate all 0.8.9-1 [35.2 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf python3-pyrle armhf 0.0.33-4+b2 [223 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf python3-pytest all 7.2.1-2 [236 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf python3-pytest-xdist all 3.1.0-1 [39.6 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf python3-sorted-nearest armhf 0.0.38+dfsg-1 [389 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf samtools armhf 1.16.1-1 [575 kB] Fetched 43.0 MB in 5s (9411 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17881 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:armhf (3.11.2-6) ... Setting up libexpat1:armhf (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18197 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18631 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_armhf.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package tzdata. Preparing to unpack .../01-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../04-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... 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Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../28-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../29-libxml2_2.9.14+dfsg-1.3~deb12u1_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. 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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../45-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../46-libcurl3-gnutls_7.88.1-10+deb12u4_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.88.1-10+deb12u4) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../47-libdeflate0_1.14-1_armhf.deb ... Unpacking libdeflate0:armhf (1.14-1) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../48-libgfortran5_12.2.0-14_armhf.deb ... Unpacking libgfortran5:armhf (12.2.0-14) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../49-libhtscodecs2_1.3.0-4_armhf.deb ... Unpacking libhtscodecs2:armhf (1.3.0-4) ... Selecting previously unselected package libhts3:armhf. 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Unpacking python3-pyrle (0.0.33-4+b2) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../74-python3-pytest_7.2.1-2_all.deb ... Unpacking python3-pytest (7.2.1-2) ... Selecting previously unselected package python3-pytest-xdist. Preparing to unpack .../75-python3-pytest-xdist_3.1.0-1_all.deb ... Unpacking python3-pytest-xdist (3.1.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../76-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-sorted-nearest. Preparing to unpack .../77-python3-sorted-nearest_0.0.38+dfsg-1_armhf.deb ... Unpacking python3-sorted-nearest (0.0.38+dfsg-1) ... Selecting previously unselected package samtools. Preparing to unpack .../78-samtools_1.16.1-1_armhf.deb ... Unpacking samtools (1.16.1-1) ... Setting up libhtscodecs2:armhf (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libpsl5:armhf (0.21.2-1) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1+deb12u1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 6 22:17:54 UTC 2024. Universal Time is now: Sat Jan 6 22:17:54 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:armhf (6.4-4) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3~deb12u1) ... Setting up bedtools (2.30.0+dfsg-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblapack3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:armhf (8.2-1.3) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.2-6) ... Setting up libcurl3-gnutls:armhf (7.88.1-10+deb12u4) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:armhf (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-natsort (8.0.2-2) ... Setting up samtools (1.16.1-1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-packaging (23.0-1) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-execnet (1.9.0-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-hypothesis (6.67.1-1) ... Setting up python3-tabulate (0.8.9-1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b3) ... Setting up python3-pytest-xdist (3.1.0-1) ... Setting up python3-pandas-lib:armhf (1.5.3+dfsg-2) ... Setting up python3-sorted-nearest (0.0.38+dfsg-1) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-pyrle (0.0.33-4+b2) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-4_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_build I: pybuild base:240: /usr/bin/python3 setup.py build echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/reproducible-path/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:307: cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/*.bed /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/test_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/tests/data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges '/build/reproducible-path/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/chip_10.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/gencode.gff3' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam' '/build/reproducible-path/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/data' '/build/reproducible-path/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/data/test_data.py' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/exons.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/bw.bw' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f1.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/cpg.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/lamina.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta2.bed' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam' '/build/reproducible-path/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam.bai' I: pybuild base:240: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build; python3.11 -m pytest -n 4 ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/reproducible-path/pyranges-0.0.111+ds plugins: hypothesis-6.67.1, xdist-3.1.0 gw0 I / gw1 I / gw2 I / gw3 I gw0 [531] / gw1 [531] / gw2 [531] / gw3 [531] FFFFFFFFFFFFFFFFFFFFFFFFFFFFF.F.....FF..FF.F.FFFF.FFFFFFFFFFF.FFFF.FFFF. [ 13%] .F.F...FFF..FF.FFFF.F.FFFFFFFFFFFFF.FFFFFFFFF.FF.FFFF.FFFFFFF..FFFFFFFFF [ 27%] .FF.....FFFFFF.FFFFFFFFFFFFF.FF.FF.FF.FF..F.FFFFFF.F.FFF.FF.FFFFFFF.FFFF [ 40%] FFFFFF.FFFFFFFFFFFFFFFFFFFFFFF.F.FFFFFFF.FF.FFFFFFFF.FFFF...FF.FF.FF.FF. [ 54%] FFF.FFFFFFF.FFF.FF.FFFFF..FFF.FF.FFFFFFFFFFFFFFFF..F.FFFFFFFFFFF.F.FFF.. [ 67%] .FFF.FFF..F.F.FF..F.FFFFF.FF.FFFFFFFFFFFFFFFFFFFFFFFFFF.FFFFFFFFF.FFFFFF [ 81%] FF.FFFFFF..FF..FFFF.FFFF.FFFFFF.F.FFFFFFFF..FFFFFF..F.F.FFFFFFFF.FFF.... [ 94%] .....FFF.F.F.FF..F.FF.F.... [100%] =================================== FAILURES =================================== __________________________ test_set_intersect[False] ___________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpcd083ary/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpcd083ary/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp8rv_hey5/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8rv_hey5/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpzx10k2ex/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpzx10k2ex/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp3i5pto1f/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3i5pto1f/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpfpayo3md/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfpayo3md/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpycedt6jv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpycedt6jv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpafw2oe23/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpafw2oe23/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmper5247x8/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmper5247x8/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpos368ezf/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpos368ezf/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpaejmevib/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpaejmevib/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmppcji1mmt/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmppcji1mmt/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp1l3ycqy6/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1l3ycqy6/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpdzx8_jx_/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpdzx8_jx_/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpbh6dwfyk/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbh6dwfyk/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp4r8y0sgi/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp4r8y0sgi/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpv2ge94g1/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv2ge94g1/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpjpyp63qn/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpjpyp63qn/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpy8pgai84/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy8pgai84/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxus11ndz/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxus11ndz/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpot1g03c7/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpot1g03c7/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmphjcxzmjb/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmphjcxzmjb/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpq5n5noao/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq5n5noao/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpxikt70lv/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxikt70lv/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmpn2vswuua/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpn2vswuua/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp92ve1agl/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp92ve1agl/f2.bed | bedtools merge -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -a <(sort -k1,1 -k2,2n /tmp/tmp9cv7qade/f1.bed | bedtools merge -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp9cv7qade/f2.bed | bedtools merge -c 4,5,6 -o first -i -) ____________ test_three_in_a_row[strandedness_chain2-method_chain2] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ___________ test_three_in_a_row[strandedness_chain35-method_chain35] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ____________ test_three_in_a_row[strandedness_chain3-method_chain3] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ___________________________ test_set_intersect[same] ___________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:113: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:128: in test_set_intersect result = gr.set_intersect(gr2, strandedness=strandedness) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_intersect( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpwqy1hwjx/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpwqy1hwjx/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpi9hak96c/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpi9hak96c/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpbwmi8atp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpbwmi8atp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpd00vpzye/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpd00vpzye/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp8iieb49j/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp8iieb49j/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpxjiequrw/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpxjiequrw/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpq1naejwk/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpq1naejwk/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpz_jfk_wf/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpz_jfk_wf/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpslnkf4s7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpslnkf4s7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp1jgjop50/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp1jgjop50/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpa_o7vzd6/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpa_o7vzd6/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpikti8wby/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpikti8wby/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpy3gj14_2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpy3gj14_2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpemzxw24z/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpemzxw24z/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp17kadp7z/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp17kadp7z/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp3y3m8_rp/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp3y3m8_rp/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpw_iribiu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpw_iribiu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpg2o4h4zs/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpg2o4h4zs/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpfymjkfya/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpfymjkfya/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmptbai2d3t/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmptbai2d3t/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpnknkwzk2/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpnknkwzk2/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp32rzjbs7/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp32rzjbs7/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp25sowc6x/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp25sowc6x/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpv72evt8m/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpv72evt8m/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmpov0uze81/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmpov0uze81/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) cmd cmd cmd cmd cmd bedtools intersect -s -a <(sort -k1,1 -k2,2n /tmp/tmp7pt_xiqu/f1.bed | bedtools merge -s -c 4,5,6 -o first -i -) -b <(sort -k1,1 -k2,2n /tmp/tmp7pt_xiqu/f2.bed | bedtools merge -s -c 4,5,6 -o first -i -) ___________ test_three_in_a_row[strandedness_chain36-method_chain36] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ____________ test_three_in_a_row[strandedness_chain4-method_chain4] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ___________________ test_nearest[downstream-False-opposite] ____________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = False, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:115: in _nearest r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, pyranges/methods/nearest.py:62: in _next_nonoverlapping r_idx, dist = nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=False, E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:34: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi6i1nuw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6i1nuw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl23n_i9b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl23n_i9b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnngchrzb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnngchrzb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyczikgdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyczikgdh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpye4_ysvm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpye4_ysvm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizwvb6ta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizwvb6ta/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ptoqps0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ptoqps0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp5w29ynx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp5w29ynx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3u99uhpq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3u99uhpq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps8utdo46/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps8utdo46/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7napg6hd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7napg6hd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpztm04qwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpztm04qwo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwnyyjmj6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwnyyjmj6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz6enm09k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz6enm09k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpais46xb3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpais46xb3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm_as7a07/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_as7a07/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_mfoisi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_mfoisi2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnwt4zhu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwt4zhu_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgdfwcrpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdfwcrpe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_60ak2m_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_60ak2m_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7xwuzd7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xwuzd7y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyvkpugky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvkpugky/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqs9au9pv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqs9au9pv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppdsd7l0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppdsd7l0v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd08jpj_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd08jpj_h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvtr2vp7s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtr2vp7s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph_6edlaz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_6edlaz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0kupsfl_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0kupsfl_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6no506qd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6no506qd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbmu3yi43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbmu3yi43/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfybwgrjt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfybwgrjt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwmbl6qmn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmbl6qmn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuaabjehg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuaabjehg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_os130bi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_os130bi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4507ai9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4507ai9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjyxjupx8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjyxjupx8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkni7xx39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkni7xx39/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmezq549y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmezq549y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaolzr53t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaolzr53t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa0351czf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0351czf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ys4xpiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ys4xpiz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp90gmkxmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90gmkxmz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpitsw6w_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitsw6w_m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpveofriby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpveofriby/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdpk1iewe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdpk1iewe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbuuo8_um/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbuuo8_um/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg4fxtao6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg4fxtao6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2g3ucqwm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2g3ucqwm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkyxl3ut4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyxl3ut4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1411f4nc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1411f4nc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr73rxn3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr73rxn3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxeojgiph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeojgiph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjpkrs8xj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpkrs8xj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ep7rnrw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ep7rnrw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5gq8t95x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gq8t95x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr_9s6e5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr_9s6e5m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbeve0kyk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbeve0kyk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjhq907s7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhq907s7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbndp0l1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbndp0l1d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw88gd_0a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw88gd_0a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_8pwk3yf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_8pwk3yf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpflyswmv7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflyswmv7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoaqrh5kx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoaqrh5kx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvp3t19w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvp3t19w8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwhm50qtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwhm50qtp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl36_tzid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl36_tzid/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0xt_yri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0xt_yri/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4geirmi9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4geirmi9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjli8k2eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjli8k2eg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm0srkw8v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0srkw8v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiq1oa_ut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiq1oa_ut/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1zhflin/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1zhflin/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp88wge9ry/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp88wge9ry/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_waoncay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_waoncay/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk_06btno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_06btno/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpht1akw8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpht1akw8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpunu832h1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunu832h1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsjzwfg3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjzwfg3i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2iic78t9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2iic78t9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2bflnbmb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2bflnbmb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6b29q2k2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6b29q2k2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjt0x3tu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt0x3tu2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgv0h0r9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgv0h0r9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpplz2ou7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplz2ou7a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsn1xktzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsn1xktzr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn4wlkmz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4wlkmz6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpijfkiwdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijfkiwdo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp75bjysue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75bjysue/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5_fplp92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5_fplp92/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2p8y8d80/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2p8y8d80/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpih2ayluc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpih2ayluc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1l3sbooa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1l3sbooa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdrsampfo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrsampfo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujzskyj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujzskyj3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiscqlygv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiscqlygv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnrpfuesf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnrpfuesf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuqcol1vg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqcol1vg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_wnjl8sp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_wnjl8sp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj4cgnzqb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj4cgnzqb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcz7a15d4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcz7a15d4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpksvillrj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksvillrj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_k3_9b6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_k3_9b6w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwvm74l35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvm74l35/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzbrdtfu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzbrdtfu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkxewg5j8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxewg5j8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptkol5axt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptkol5axt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyowyvmi2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyowyvmi2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1vew10p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1vew10p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsk1ukpdw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsk1ukpdw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfepqctk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfepqctk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp423cqkug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp423cqkug/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxzmjdiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxzmjdiu/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________________ test_set_union[False] _____________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmprt7sabcb/f1.bed /tmp/tmprt7sabcb/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfzlji_dm/f1.bed /tmp/tmpfzlji_dm/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1r6v7c0k/f1.bed /tmp/tmp1r6v7c0k/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp3ap194p7/f1.bed /tmp/tmp3ap194p7/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp6_g5zkwg/f1.bed /tmp/tmp6_g5zkwg/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpj1ei1u27/f1.bed /tmp/tmpj1ei1u27/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpth6svq06/f1.bed /tmp/tmpth6svq06/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfvk3bb1a/f1.bed /tmp/tmpfvk3bb1a/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmefjsr5y/f1.bed /tmp/tmpmefjsr5y/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp93cnsm6c/f1.bed /tmp/tmp93cnsm6c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpna349t6e/f1.bed /tmp/tmpna349t6e/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2c8f1wxc/f1.bed /tmp/tmp2c8f1wxc/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp94e_iuo6/f1.bed /tmp/tmp94e_iuo6/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpovqspo_c/f1.bed /tmp/tmpovqspo_c/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpnim12reh/f1.bed /tmp/tmpnim12reh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_tclhpne/f1.bed /tmp/tmp_tclhpne/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1pu7v6wh/f1.bed /tmp/tmp1pu7v6wh/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmphg3iy8u5/f1.bed /tmp/tmphg3iy8u5/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpa2i0wcng/f1.bed /tmp/tmpa2i0wcng/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp7q81bdrs/f1.bed /tmp/tmp7q81bdrs/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp2n7mefdr/f1.bed /tmp/tmp2n7mefdr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpymucslgn/f1.bed /tmp/tmpymucslgn/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9m732d82/f1.bed /tmp/tmp9m732d82/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpyx008zyr/f1.bed /tmp/tmpyx008zyr/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpfuvql62o/f1.bed /tmp/tmpfuvql62o/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpl5y0vl3q/f1.bed /tmp/tmpl5y0vl3q/f2.bed | bedtools sort | bedtools merge -c 4,5,6 -o first -i - ____________ test_three_in_a_row[strandedness_chain5-method_chain5] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') _____________________________ test_jaccard[False] ______________________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception _____________________________ test_set_union[same] _____________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:134: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:149: in test_set_union result = gr.set_union(gr2, strandedness=strandedness) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_set_union( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd cat /tmp/tmp52qct265/f1.bed /tmp/tmp52qct265/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp8lxviiru/f1.bed /tmp/tmp8lxviiru/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdst7dsuo/f1.bed /tmp/tmpdst7dsuo/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1r6fuypz/f1.bed /tmp/tmp1r6fuypz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5824nx3_/f1.bed /tmp/tmp5824nx3_/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpif9_i0wx/f1.bed /tmp/tmpif9_i0wx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp91pgvwoz/f1.bed /tmp/tmp91pgvwoz/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpt2mit9i5/f1.bed /tmp/tmpt2mit9i5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpmxloxavn/f1.bed /tmp/tmpmxloxavn/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpqeuyvock/f1.bed /tmp/tmpqeuyvock/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpdgr2wy37/f1.bed /tmp/tmpdgr2wy37/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp9hak93vk/f1.bed /tmp/tmp9hak93vk/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_up_vy3t/f1.bed /tmp/tmp_up_vy3t/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpz0r68nm5/f1.bed /tmp/tmpz0r68nm5/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpsczdjqjx/f1.bed /tmp/tmpsczdjqjx/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp39tqg699/f1.bed /tmp/tmp39tqg699/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpe70shjbg/f1.bed /tmp/tmpe70shjbg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpws0kmf3m/f1.bed /tmp/tmpws0kmf3m/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpo1rwr1br/f1.bed /tmp/tmpo1rwr1br/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpwp89s0eg/f1.bed /tmp/tmpwp89s0eg/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp1b2ty_i4/f1.bed /tmp/tmp1b2ty_i4/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpkisi23nt/f1.bed /tmp/tmpkisi23nt/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp_xn7hbf1/f1.bed /tmp/tmp_xn7hbf1/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmpu4zgqrc9/f1.bed /tmp/tmpu4zgqrc9/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmp5hi88rti/f1.bed /tmp/tmp5hi88rti/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - cmd cmd cmd cmd cmd cat /tmp/tmps97w62wy/f1.bed /tmp/tmps97w62wy/f2.bed | bedtools sort | bedtools merge -s -c 4,5,6 -o first -i - ___________ test_three_in_a_row[strandedness_chain37-method_chain37] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2CAA0YGLAAAADUAAg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain6-method_chain6] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ______________________________ test_jaccard[same] ______________________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", no_opposite) tests/test_binary.py:363: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:378: in test_jaccard result = gr.stats.jaccard(gr2, strandedness=strandedness) pyranges/statistics.py:766: in jaccard for v in self.set_intersect(other).lengths(as_dict=True).values()) pyranges/pyranges.py:3687: in set_intersect self_clusters = self.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_jaccard( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ____________ test_three_in_a_row[strandedness_chain7-method_chain7] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ____________ test_three_in_a_row[strandedness_chain8-method_chain8] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain38-method_chain38] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________ test_three_in_a_row[strandedness_chain9-method_chain9] ____________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ___________ test_three_in_a_row[strandedness_chain10-method_chain10] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ___________ test_three_in_a_row[strandedness_chain39-method_chain39] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain11-method_chain11] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ___________ test_three_in_a_row[strandedness_chain12-method_chain12] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ___________ test_three_in_a_row[strandedness_chain40-method_chain40] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 9943138 | 9951367 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 9943138 | 9951367 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ___________ test_three_in_a_row[strandedness_chain13-method_chain13] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ___________ test_three_in_a_row[strandedness_chain41-method_chain41] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ___________ test_three_in_a_row[strandedness_chain14-method_chain14] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain42-method_chain42] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ___________ test_three_in_a_row[strandedness_chain15-method_chain15] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain43-method_chain43] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain45-method_chain45] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 215576 | 217062 | a | 0 | + | E | chr1 | 66057 | 67543 | a | 0 | - | E | chr1 | 262405 | 263891 | a | 0 | - | E | chr1 | 4098 | 5584 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr1 | 262405 | 262668 | a | 0 | - | E | chr1 | 262405 | 263891 | a | 0 | - | E | chr1 | 262405 | 263891 | a | 0 | - | E | chr1 | 262405 | 263891 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 215576 | 217062 | a | 0 | + | E | chr1 | 920322 | 921808 | a | 0 | - | E | chr1 | 920322 | 921808 | a | 0 | - | E | chr1 | 920322 | 921808 | a | 0 | - | E | ... | ... | ... | ... | ... | ... | E | chr1 | 920322 | 920585 | a | 0 | - | E | chr1 | 920322 | 921808 | a | 0 | - | E | chr1 | 920322 | 921355 | a | 0 | - | E | chr1 | 920322 | 924164 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 68098 | 72973 | a | 0 | + | E | chr1 | 68098 | 71184 | a | 0 | + | E | chr1 | 68098 | 71176 | a | 0 | + | E | chr11 | 7152386 | 7152653 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('join', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXiclY69DcIwEEbvxbGTOHHCjwQNoqEBJMQCIKBlAEokBqClZwcGYAb2YBEqJFoKzg01uLqf794zw/HtyvR8cRQkAkgPQVLYHN605fRkP1n2kXnzALd4iT4IZquzQJJjkJaepKQ5boCTnb1jIVNW5OlGM4rX7n9bJEWhWr5ePanLSGwg/0U7owx0yFaURQ3W4mOGJOZEPKY5jpAar7O6shgTy6oKsu56/anIB9hsGaM=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain19-method_chain19] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 66050 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AAABAAA0AGwBIQAAAQMBegAAAAAAAAQBAAAABwIAAQABAA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain47-method_chain47] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain21-method_chain21] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain49-method_chain49] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ___________ test_three_in_a_row[strandedness_chain22-method_chain22] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 258 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkYGBgYmRgBCJtEMkAEoBSDAAEAQA4') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain50-method_chain50] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain51-method_chain51] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ___________ test_three_in_a_row[strandedness_chain52-method_chain52] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ___________ test_three_in_a_row[strandedness_chain23-method_chain23] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 514 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 196865 | 197125 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY3RlvBfGwM/EwMjNyCDFwMjAwMAGIhgDYycdBlIMjMxgLjMDCHBp8oB4DACPuQQK') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain53-method_chain53] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ___________ test_three_in_a_row[strandedness_chain54-method_chain54] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ___________ test_three_in_a_row[strandedness_chain55-method_chain55] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ___________ test_three_in_a_row[strandedness_chain24-method_chain24] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131335 | 131592 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65799 | 67080 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicFYq5DQAwDITA+arsk/0ny5kKIZxsQV65uVH02EmGabhoKlbm/BIdAII=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain56-method_chain56] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ___________ test_three_in_a_row[strandedness_chain57-method_chain57] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain25-method_chain25] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 76298 | 76300 | a | 0 | + | E | chr1 | 76298 | 76300 | a | 0 | - | E | chr1 | 76298 | 76300 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65538 | 65539 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicYzSect2O0Tyq+iBjUIqTCAMDIwMjoxYnmAIDJqAQExCyMDKAASMYMoAxWBWQAgAzXQUM') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain58-method_chain58] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ___________ test_three_in_a_row[strandedness_chain59-method_chain59] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ___________ test_three_in_a_row[strandedness_chain60-method_chain60] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ___________ test_three_in_a_row[strandedness_chain26-method_chain26] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain61-method_chain61] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ___________ test_three_in_a_row[strandedness_chain62-method_chain62] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ___________ test_three_in_a_row[strandedness_chain27-method_chain27] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 14338 | 14596 | a | 0 | - | E | chr1 | 65538 | 65796 | a | 0 | - | E | chr1 | 258 | 516 | a | 0 | - | E | chr7 | 66817 | 67081 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 265474 | 265733 | a | 0 | - | E | chr1 | 265474 | 265733 | a | 0 | - | E | chr1 | 265474 | 265733 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', False), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicJYzBDYAwDANzoYXy6AZMwLuPSkjMwP4PZsEJD1vK2TEUDkZ7L857Dl2YSatsCYNONVxMic0gbBFkyC5VcGtRSOQxUTr2COfbX/4AEbMDZg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain63-method_chain63] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ___________ test_three_in_a_row[strandedness_chain28-method_chain28] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain64-method_chain64] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain29-method_chain29] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain66-method_chain66] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 459009 | 463362 | a | 0 | + | E | chr1 | 66562 | 70915 | a | 0 | - | E | chr1 | 66055 | 70408 | a | 0 | - | E | chr1 | 71426 | 75779 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66562 | 67075 | a | 0 | + | E | chr1 | 66055 | 66312 | a | 0 | + | E | chr1 | 1179911 | 1180424 | a | 0 | + | E | chr1 | 460037 | 460550 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 34 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXichYyxCYBAEAR3Tv1PTBRBBME6rMPMRIxswGJszHIE70IjL5iFZW/Ya4NtXE4K1tmRbgk0UIKRUYQljx6pESZfRR34eW9J3uWq/Ehc4Ti655IrFIdMk/QC6GEJfQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain31-method_chain31] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 265 | 779 | a | 0 | + | E | chr1 | 6199291 | 6199805 | a | 0 | - | E | chr1 | 1143639 | 1144153 | a | 0 | - | E | chr1 | 265 | 779 | a | 0 | - | E | chr1 | 265 | 779 | a | 0 | - | E | chr1 | 265 | 779 | a | 0 | - | E | chr13 | 265 | 779 | a | 0 | - | E | chr14 | 265 | 779 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 8 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6199291 | 6199549 | a | 0 | - | E | chr1 | 6199291 | 6199822 | a | 0 | - | E | chr2 | 6199291 | 6199549 | a | 0 | - | E | chr2 | 6199291 | 6199549 | a | 0 | - | E | chr2 | 6199291 | 6199549 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65538 | 65796 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2bMZIwWYGFkDHXuZWX0kD98mDEsonUOo53HZndG5p5VExl9mqNyGK0ZU24yMAKVMTHwMrIyMjIy8DAwMDAy2MdN/8XIrC5YHAbicjAwMjEysgNZzIwgY1iwGwPSDzSBAWECIwuTEFCYQRwozMjIysPGyABEIMgOIhiEgSpAGgAcgBnr') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain68-method_chain68] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 258 | 515 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BgMdV9GFCoJMrAwAiGEApMMzAAADmYAkg=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________ test_k_nearest[downstream-False-opposite-last] ________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = False, strandedness = 'opposite' ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=False, E strandedness='opposite', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGOGBkxBBiAAAAngAG') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd4bldlt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4bldlt1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqyut5pkr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqyut5pkr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9gmswipf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9gmswipf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp050p07ts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp050p07ts/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpffqmun9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffqmun9k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_eqzngom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_eqzngom/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp292y50pm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp292y50pm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdq_p4l2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdq_p4l2v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzi1_id2g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzi1_id2g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzhkukgwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhkukgwz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoda56ixv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoda56ixv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwg7gsne2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwg7gsne2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3e60xsul/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3e60xsul/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxks335ug/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxks335ug/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpguom886u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpguom886u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp83ku76mh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83ku76mh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph569e0bx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph569e0bx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvl6oa1o8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvl6oa1o8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkwd6tdhr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkwd6tdhr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkuqgpoyl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkuqgpoyl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5rlthmtu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5rlthmtu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyx3c4wz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyx3c4wz_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9vy7kgk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9vy7kgk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn5a_lz2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn5a_lz2f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvh8ht4r6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvh8ht4r6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps_ruip91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_ruip91/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcp5hr1t1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcp5hr1t1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr5uvzqga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr5uvzqga/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtryyykh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtryyykh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnhhnefzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhhnefzf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2uqgnjc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2uqgnjc1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp02j1_852/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp02j1_852/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfro05l6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfro05l6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp774q8kk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp774q8kk3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxy0ptrgz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxy0ptrgz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcq_8uthp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcq_8uthp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz7yuxogy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7yuxogy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzcfksjnk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzcfksjnk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7h2g9vl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7h2g9vl1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbml9k3ym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbml9k3ym/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk5asbufd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk5asbufd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx51ujnm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx51ujnm2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeo1pt20a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeo1pt20a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk0g61dsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0g61dsn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpely7d1qh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpely7d1qh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxct0smig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxct0smig/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7mfq__ar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mfq__ar/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoe_5hwpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoe_5hwpl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvih95i95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvih95i95/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1i2qyhx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1i2qyhx0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_li5z304/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_li5z304/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpebpv06f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebpv06f5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmj2ljcp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmj2ljcp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgzmonu4u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzmonu4u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_eugp42b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_eugp42b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfdp0bkz4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdp0bkz4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcoy5nrhn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcoy5nrhn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8quwloh8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8quwloh8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr0fp4vue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0fp4vue/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnpz6_y4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnpz6_y4a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcn5q88r7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcn5q88r7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe79qqycf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe79qqycf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9_1mmx66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_1mmx66/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg3e3xzaj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3e3xzaj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq83owbf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq83owbf9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph9ou2pgy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9ou2pgy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpek_azi26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpek_azi26/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy_zqiuwo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_zqiuwo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpud14fptd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpud14fptd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ho0j2ki/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ho0j2ki/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphn1h493b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphn1h493b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprbssgzte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbssgzte/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8m38kvmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8m38kvmo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5ursbks_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5ursbks_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9pp7geir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pp7geir/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1o5nha99/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o5nha99/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5wn__tze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5wn__tze/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_meloz1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_meloz1u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr56r27xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr56r27xp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu8uygxra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8uygxra/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu5z_ywck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5z_ywck/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7qp6keu0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qp6keu0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgyjxqqii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyjxqqii/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpme5sqpcs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpme5sqpcs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprfx22gt8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprfx22gt8/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain33-method_chain33] ___________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-False-same-last] __________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = False, strandedness = 'same' ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=False, E strandedness='same', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:56: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcqej61zt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqej61zt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvd_kr_zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvd_kr_zj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnsoe_5nz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsoe_5nz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpktml8nwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktml8nwn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptnadh648/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnadh648/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4nt6wr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4nt6wr0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb5dyeswu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb5dyeswu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf9263ng6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9263ng6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxndhrf90/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxndhrf90/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbgwr4e_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgwr4e_s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_2hujkaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2hujkaf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5cayqz2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5cayqz2z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp42y03vms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42y03vms/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_frw0cq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_frw0cq8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfccj_86z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfccj_86z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl_k_fg6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_k_fg6g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi2kgk2lr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi2kgk2lr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwcg6zod1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwcg6zod1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprq5mlpez/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprq5mlpez/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdozlxrux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdozlxrux/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvshbtaq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvshbtaq_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjk3ub0uu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjk3ub0uu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg7birf2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7birf2m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1o167oxb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1o167oxb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgpwyr07s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpwyr07s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2083ziyc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2083ziyc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphmv2qts0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmv2qts0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjpmh5qtt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpmh5qtt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwcltq3_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwcltq3_t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsmhikprh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsmhikprh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfdv9s4e9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfdv9s4e9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvtm6juit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtm6juit/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphy6h9ss0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphy6h9ss0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1wwqp0sw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1wwqp0sw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3aoa1nl7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3aoa1nl7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0hs4no_s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hs4no_s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbudfikhw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbudfikhw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw1zk3eur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw1zk3eur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps85ysnq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps85ysnq2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprpcfi7dv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprpcfi7dv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdttu0dwb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdttu0dwb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprakkadsh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprakkadsh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0_ekr9km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0_ekr9km/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpchpdbmuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchpdbmuh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbpxmruu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpxmruu2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptqwfanfr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqwfanfr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdqpwr2qr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdqpwr2qr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsx1geda4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsx1geda4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp791x478n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp791x478n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpex6not56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpex6not56/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpworoo8yj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpworoo8yj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx1536rdr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx1536rdr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqakav6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqakav6j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn3qa8283/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn3qa8283/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn4dhb45_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4dhb45_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6c9vjhzf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6c9vjhzf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvss6one3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvss6one3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsikquhyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsikquhyn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplo9_xv0e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplo9_xv0e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2asmhiel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2asmhiel/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain70-method_chain70] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________ test_k_nearest[downstream-False-False-last] __________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=False, E strandedness=False, E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:56: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy9dlmx5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9dlmx5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxytvs1kt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxytvs1kt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3kzhqefe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kzhqefe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu3lh71um/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3lh71um/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphfcr3i5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphfcr3i5_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmsnr1dmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmsnr1dmd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpro5zslpu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpro5zslpu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjgpqh603/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgpqh603/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgebrkygz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgebrkygz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprztkqmc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprztkqmc8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvr99_yvt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvr99_yvt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz913gu7j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz913gu7j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmbf611hf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbf611hf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdk1fs2y7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdk1fs2y7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp76fbdzfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp76fbdzfm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9qv6xfe6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9qv6xfe6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt5whfwxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt5whfwxr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8kc8566f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8kc8566f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4kkwncda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4kkwncda/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2el5uu7f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2el5uu7f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6u5dvhro/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6u5dvhro/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6emo1n8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6emo1n8a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzl0nojep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzl0nojep/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9tjs6w98/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tjs6w98/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnzaruddu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnzaruddu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt7vxg2_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt7vxg2_q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpti5ua8bu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpti5ua8bu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmlynmv9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlynmv9i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkrhhv4tq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrhhv4tq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqdzon0ts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdzon0ts/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9c5gw9ay/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9c5gw9ay/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1im_tp4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1im_tp4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp37scdch5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37scdch5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmaibqqvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmaibqqvs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwx5mmhk5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwx5mmhk5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy__dxzde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy__dxzde/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjcwimnlt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjcwimnlt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6vs2z1pq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vs2z1pq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpofgiklct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofgiklct/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8tqzd199/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8tqzd199/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa912fg_m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa912fg_m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyq7zmqnz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyq7zmqnz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpexdx6cde/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpexdx6cde/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf4iyn3cb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4iyn3cb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbs9y_9in/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbs9y_9in/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmputb00m2s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputb00m2s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph1xquuvq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1xquuvq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1qnepi1w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1qnepi1w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpttfw9yt0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpttfw9yt0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwraegf78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwraegf78/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprwytxl9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwytxl9m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt1hkp8ei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1hkp8ei/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg52c988v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg52c988v/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain71-method_chain71] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain117-method_chain117] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ________________ test_k_nearest[downstream-True-opposite-last] _________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = True, strandedness = 'opposite' ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=True, E strandedness='opposite', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:56: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpukpggkip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukpggkip/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpumemantp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumemantp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp59cxwe77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp59cxwe77/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpogi_qrlc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogi_qrlc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpramqnosa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpramqnosa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn0k4y0zs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0k4y0zs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp597bs0pk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp597bs0pk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfgitrb9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfgitrb9t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi0c835om/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0c835om/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprbilzs4e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbilzs4e/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppm1d671c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppm1d671c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp34y_lq83/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34y_lq83/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv3mkny8f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3mkny8f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_4ptuc0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4ptuc0d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbgtputfw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbgtputfw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdkwiq5uz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkwiq5uz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5s9kvmo8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5s9kvmo8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph450pte2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph450pte2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy14ocqq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy14ocqq6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9sfrvll4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sfrvll4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3kr1vatk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kr1vatk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyp52ujca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyp52ujca/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb44js4fd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb44js4fd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpelp29m_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelp29m_t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt4d7whxj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4d7whxj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp49df_qoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp49df_qoh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprsfmfbmv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprsfmfbmv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp55c5c3nu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55c5c3nu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpweuhwfca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpweuhwfca/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz74amp68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz74amp68/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjv02pfsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjv02pfsm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4dzkt8nl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dzkt8nl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpytuld9z4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpytuld9z4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaml_qhu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaml_qhu3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5jracl0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jracl0s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjqq4hk5y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqq4hk5y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe9eobe8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9eobe8x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmporofjtmp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporofjtmp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps3bk7els/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3bk7els/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymlgfpcx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymlgfpcx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6d_8jzh3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6d_8jzh3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa8gnhsg1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8gnhsg1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm0ezvazr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm0ezvazr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68ajdqs6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68ajdqs6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp399ts9zi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp399ts9zi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpurbkyo1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpurbkyo1u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp41ndaxep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp41ndaxep/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdiyi_2vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdiyi_2vr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ibm7amo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ibm7amo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwl86t_oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwl86t_oo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjt5c1ujz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt5c1ujz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuv4gwzfl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuv4gwzfl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_1jdpebe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1jdpebe/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6cjz49mx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6cjz49mx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0rsuppbq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rsuppbq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc4flyju3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc4flyju3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl686f4_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl686f4_u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqv9xifmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqv9xifmo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp93g9qs0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93g9qs0d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphdmg9rto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphdmg9rto/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8fn3kqur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8fn3kqur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz2k2b0s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz2k2b0s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe0b0drjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0b0drjy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbej_cztx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbej_cztx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg0671jwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg0671jwg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpopiu0wqu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpopiu0wqu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp31ze9zd2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31ze9zd2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2hrsqkgs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hrsqkgs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcouv6n_t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcouv6n_t/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain72-method_chain72] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 8326680 | 8326681 | a | 0 | - | E | chr1 | 852226 | 852313 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 984066 | 984323 | a | 0 | - | E | chr1 | 984066 | 984323 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RgZGBkZIzl4ABRQMygV88nDmTygngMEBAGkgPxXSr2lDKAhPlZwGpBTHaQDAgAAJWOA8g=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-True-same-last] ___________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=True, E strandedness='same', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:56: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz7m_yqo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz7m_yqo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp87e0hl89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87e0hl89/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9gdath84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9gdath84/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2n44q1xi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2n44q1xi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38ncyyr9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38ncyyr9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb_fsu881/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb_fsu881/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzj_35398/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzj_35398/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqw1ba4dj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqw1ba4dj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmlzsqh69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmlzsqh69/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb16k4au7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb16k4au7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp71stsrwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp71stsrwr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp677em_ei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp677em_ei/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp37spmpu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37spmpu_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38g32foh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38g32foh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcydr1gxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcydr1gxw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph_8fmb3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_8fmb3u/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphsl1l6vz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphsl1l6vz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo0g5i__6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0g5i__6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpplnp5wol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpplnp5wol/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ynpvjrx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ynpvjrx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpifs1emu3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifs1emu3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1heqwb__/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1heqwb__/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq0k4d13v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq0k4d13v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg_e04mm4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg_e04mm4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph9rol2sz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9rol2sz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_jdy4ls9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_jdy4ls9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9n88lhbg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9n88lhbg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptuwbk0v8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptuwbk0v8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfn5_5152/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfn5_5152/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_1a_rv7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1a_rv7k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi1foh_21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1foh_21/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5krld_pu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5krld_pu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmprx2szr_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprx2szr_h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2no4mm8d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2no4mm8d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxja989lf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxja989lf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe8hxf9nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8hxf9nt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmbt6h7i1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbt6h7i1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5e42qzeb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5e42qzeb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsmj71krf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsmj71krf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuvd7iw0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuvd7iw0y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph681cuxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph681cuxg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf48jh1v5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf48jh1v5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2y8mcods/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2y8mcods/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpigmczoum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpigmczoum/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoy5s_ptn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoy5s_ptn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpze3wls1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpze3wls1f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpej3exr96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpej3exr96/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplcvza53t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcvza53t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1zgpiijt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1zgpiijt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmc6iz8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmc6iz8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp85lmjora/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp85lmjora/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwawqmlj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwawqmlj8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv07xj4we/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv07xj4we/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxcnydces/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcnydces/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo7xh8y7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7xh8y7z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp18aq2qsd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18aq2qsd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeb8650my/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeb8650my/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnodv81ed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnodv81ed/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbkdezmgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkdezmgf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9pll5umy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pll5umy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmptf2_ymuu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptf2_ymuu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08lb3jeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08lb3jeh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplj5s8vl5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplj5s8vl5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgdqvdcg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdqvdcg8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmppu3sqtc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppu3sqtc7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd4v68cu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd4v68cu5/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr15 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain119-method_chain119] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain73-method_chain73] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY+RMPRTCwAiEIAAh0Sg0DgBIeQGM') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[downstream-True-False-last] __________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = True, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:140: in nearest_next lidx, ridx, dist = nearest_next_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:56: in nearest_next_idx lidx, ridx_pos, dist = k_nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=True, E strandedness=False, E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:56: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnyr4j8ig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyr4j8ig/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplak4sveh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplak4sveh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpii58hqvv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpii58hqvv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl8l3d_fj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl8l3d_fj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptc8uud4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptc8uud4z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuspldpk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuspldpk6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz_f0nu62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz_f0nu62/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2o54nld8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2o54nld8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp98rtgem3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98rtgem3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb8tvyd43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb8tvyd43/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7bopttvt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7bopttvt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpogshy6iz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogshy6iz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpefb1w9hb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpefb1w9hb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi1tld9f0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1tld9f0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp580ysuyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp580ysuyj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjjuq7ue6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjuq7ue6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy5a9il1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy5a9il1h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzp7gbs92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzp7gbs92/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxo6fvjw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxo6fvjw5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmn1fv6zv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmn1fv6zv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpajqgbc4o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpajqgbc4o/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjpjema0z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjpjema0z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6bf773mp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bf773mp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeviv5lcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeviv5lcl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2af2f6q5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2af2f6q5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpskq9r2b1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpskq9r2b1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpks09xn7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpks09xn7_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmuwe90ee/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmuwe90ee/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprp0ndf78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprp0ndf78/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmmm9nz8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmmm9nz8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph70fjmmm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph70fjmmm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4rl343mv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4rl343mv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyeo9pj0t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyeo9pj0t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpze_6i0yk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpze_6i0yk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7tn1ng1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7tn1ng1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe5cngf6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5cngf6b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmprikj0z5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprikj0z5c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6rn5wdy1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6rn5wdy1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp__6qkra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp__6qkra/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5xxv9mz5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5xxv9mz5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaoe33qv0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaoe33qv0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps26kzdk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps26kzdk6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2svui8p3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2svui8p3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps_skmk3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_skmk3y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp72yul9kw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72yul9kw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgyvn5oaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyvn5oaf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfp__3ycm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfp__3ycm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpea1j7cmd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpea1j7cmd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp90rusp9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90rusp9h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpywjopsuh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpywjopsuh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxb5foobb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxb5foobb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuq4yph4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuq4yph4a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7nu6syoh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7nu6syoh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwqhrfcda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqhrfcda/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5fdul6w6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5fdul6w6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp628jizup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp628jizup/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpymum3vdi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpymum3vdi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -iu -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdmyd8fzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdmyd8fzi/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain74-method_chain74] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 258 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1900802 | 1901571 | a | 0 | + | E | chr1 | 1900802 | 1901571 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RkAAFGCMXAyMDCCObmuZvMYHRobysHiTHIAuUZmYHCjFC1jIzMjAwAbU8Dgg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain120-method_chain120] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________ test_k_nearest[upstream-False-opposite-last] _________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = False, strandedness = 'opposite' ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 65794 | a | 0 | + | E | chr1 | 65793 | 65794 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=False, E strandedness='opposite', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY1TnFBVljJw6XY2BgZGBkZERRDGACTANp4AMAE0YAhE=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgnl6obmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnl6obmr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg94m2_qy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg94m2_qy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk_hcs67d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk_hcs67d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb40jkihf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb40jkihf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphw7mok04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphw7mok04/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpobu9yh8l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpobu9yh8l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe01ki2_v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe01ki2_v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy4p6xgwh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy4p6xgwh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7aueuj7u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7aueuj7u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5ur_v7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5ur_v7q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpug9l_bsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpug9l_bsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq44qd1qt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq44qd1qt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpscd0f7oh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpscd0f7oh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj62h1sik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj62h1sik/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdspdm5pb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdspdm5pb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp8jv8f5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8jv8f5w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpujzia8u2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujzia8u2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvmtcucl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmtcucl9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdzq4oigp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzq4oigp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzi_1_o2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzi_1_o2e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphua8lsi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphua8lsi_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0ejbbq89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ejbbq89/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpde4a55sh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpde4a55sh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmputjtnwu6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputjtnwu6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6va4wy2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6va4wy2w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv9qb3n14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9qb3n14/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsvxnah39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsvxnah39/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqbb3fgs0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbb3fgs0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9h1sa3sk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9h1sa3sk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdk0x250b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdk0x250b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoaa8qc0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoaa8qc0v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp224tq2dt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp224tq2dt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmbo6hdjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbo6hdjj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo86onsot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo86onsot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyq8i44cz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyq8i44cz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdvmhu281/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvmhu281/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpumfr8ugm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumfr8ugm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpja6xqh1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja6xqh1z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp939wmwz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp939wmwz_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpltcoz92t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpltcoz92t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptf8z18r7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptf8z18r7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprx0b297b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprx0b297b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpakgv6sz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpakgv6sz7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqfh0jkfy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqfh0jkfy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjk30zpvy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjk30zpvy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3futtiwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3futtiwz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6vf9bk5m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vf9bk5m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph9ne6ood/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph9ne6ood/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6r464f2w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6r464f2w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsrohd6i2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsrohd6i2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphqcu3246/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphqcu3246/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphslpjshv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphslpjshv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqj8gq_la/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqj8gq_la/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvvvmbjwr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvvvmbjwr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz6gbag60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz6gbag60/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzt7u55b0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzt7u55b0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv7dclngd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv7dclngd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp66i5jwsp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66i5jwsp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw3i07nse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3i07nse/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpls7657k_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpls7657k_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn6gfid0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6gfid0y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp30mfflxx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp30mfflxx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8h92qonr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8h92qonr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0xq_734s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xq_734s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpav_8_t8p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpav_8_t8p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2hv23ad5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hv23ad5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppl4xorp_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppl4xorp_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4nik_i3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4nik_i3c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjzfskuq0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjzfskuq0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5hdfsnpj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hdfsnpj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi_r6fcnm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_r6fcnm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe70xkp8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe70xkp8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr8krm4ip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8krm4ip/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvt_4jor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvt_4jor/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdlnpm4k3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdlnpm4k3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyefhc42u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyefhc42u/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr16 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr10 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain75-method_chain75] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain121-method_chain121] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9534233 | 9542060 | a | 0 | - | E | chr1 | 2046275 | 2054102 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 66166 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY5TPcE1lZA/IXMTACIQMQCwysVqCkTFO3tKJgaFQbhIDI2O8K1gSKM0IwgyMTCUMEBFGUUYgAABPBwcs') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________ test_k_nearest[upstream-False-same-last] ___________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = False, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=False, E strandedness='same', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjq7qmio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjq7qmio/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5akxx_sy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5akxx_sy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0pv2yrcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pv2yrcm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjmia2jey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjmia2jey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjup_iv65/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjup_iv65/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl7g4ft5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl7g4ft5_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1zushri/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1zushri/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq52b4wzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq52b4wzj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgqc8kuqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqc8kuqf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo7s5spr9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo7s5spr9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi_bnc6ah/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_bnc6ah/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq3c08e21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq3c08e21/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk7cpt2q9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk7cpt2q9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphmgqujyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphmgqujyw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqseyfvhq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqseyfvhq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpacn8c4x5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpacn8c4x5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgpdqkduj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpdqkduj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpor_vx3y1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpor_vx3y1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppe0tk5gu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppe0tk5gu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsjallq1w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsjallq1w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4f6b1ye4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4f6b1ye4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoxil3t7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxil3t7l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg3efeekn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3efeekn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzjqht10q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjqht10q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp31erpd00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31erpd00/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu3exr9mg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3exr9mg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1dsz022/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1dsz022/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa8nfhm8e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa8nfhm8e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa3u5_uzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3u5_uzq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpffxbuez5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffxbuez5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl9lxp4jg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9lxp4jg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplb0w49wh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplb0w49wh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvrm_cabx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvrm_cabx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl6h0t469/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl6h0t469/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplc1rb3_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplc1rb3_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnqgqbw34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnqgqbw34/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp675h8lbo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp675h8lbo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppg113jg_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppg113jg_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmperps6wpo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperps6wpo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzz6mzpcf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzz6mzpcf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdy5g60vo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdy5g60vo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpozizg5k_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpozizg5k_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjd46_ihm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjd46_ihm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpam5tw44s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpam5tw44s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptman1a1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptman1a1s/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_jkeyym/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_jkeyym/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi1lokyed/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi1lokyed/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnzostz8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnzostz8h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabu170hh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabu170hh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqkte4rd9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkte4rd9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdihhf1wx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdihhf1wx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9if5312/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9if5312/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain76-method_chain76] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 459009 | 459010 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 66307 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY/S39BRiYGBkYGRnBFFAzBgnksoKZjOCMBMjRNjIUEWTW4URAEitArc=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain122-method_chain122] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 65794 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2162690 | 2162692 | a | 0 | - | E | chr1 | 1310722 | 1310980 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RgZAACIMEIZoDoMPszMxjLGBiZQRxGBhGgrKoiiMnMCAFQDQxQHQwMAIN+Auo=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +13 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 10000000 | 10008425 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 18 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 13 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance, ... (+ 6 more.) ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________ test_k_nearest[upstream-False-False-last] ___________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=False, E strandedness=False, E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2v8zxceh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2v8zxceh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_9px1eg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_9px1eg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi7nsm12f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi7nsm12f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdzbys3j5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzbys3j5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmph3euj5mw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph3euj5mw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkoyx0kgv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkoyx0kgv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1z2buos7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1z2buos7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmps5i6t7b1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5i6t7b1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp7digy40/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp7digy40/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyu1bww01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyu1bww01/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi_t1g7j4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_t1g7j4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx_he4_fj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx_he4_fj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzkruf8zl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkruf8zl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsp56hikh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsp56hikh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa0ncywe9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa0ncywe9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkixi_l1f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkixi_l1f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuabztv2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuabztv2m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3cex50f8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cex50f8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfvnl1lkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfvnl1lkv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaj5m5eq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaj5m5eq_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplv6mrwpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplv6mrwpl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbl58vfkb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbl58vfkb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpms_hv0n1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpms_hv0n1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3vf1p3uu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vf1p3uu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfcza88xh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfcza88xh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgxfcqv7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxfcqv7_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjz0quys1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjz0quys1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyvo6xb2y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyvo6xb2y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmnikxi3a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnikxi3a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmply6goita/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmply6goita/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfx9ggxny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfx9ggxny/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuyqaexzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyqaexzn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5t7rknfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5t7rknfc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjfcnm298/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjfcnm298/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcrh959j4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcrh959j4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjghmb4r0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjghmb4r0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn97g0exo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn97g0exo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpug4qmyiu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpug4qmyiu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwty6md2j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwty6md2j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv5zqrift/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5zqrift/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_x4wdm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_x4wdm3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpivbwt_mn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivbwt_mn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpidvq2g_l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpidvq2g_l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz0aymmmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0aymmmr/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpippbbxkn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpippbbxkn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpufusvtnl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpufusvtnl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyiu4j2cu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyiu4j2cu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6nrfn2pw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6nrfn2pw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphauxsya_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphauxsya_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6_gi96_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_gi96_k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq5zxt4jo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5zxt4jo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0iz2yv09/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0iz2yv09/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain77-method_chain77] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain123-method_chain123] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9078844 | 9080135 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 75417 | 75675 | a | 0 | + | E | chr1 | 75417 | 75675 | a | 0 | + | E | chr1 | 75417 | 75675 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY3RmZGRkYABi164OawYGB1YuIBfEB0JGRptYRkcGJpACIE9tBgNYMYjDYKLK+IEBAJpsBSA=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_coverage[False] _____________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_aic9qlg/f1.bed -b /tmp/tmp_aic9qlg/f2.bed Chromosome Start End Name Score Strand 0 chr1 5894320 5899306 a 0 - Chromosome Start End Name Score Strand 0 chr1 1236845 1242523 a 0 + 1 chr1 4665054 4673692 a 0 + 2 chr1 872701 876280 a 0 + 3 chr1 4919218 4920265 a 0 + 4 chr1 2523142 2528861 a 0 + 5 chr3 6678993 6686966 a 0 + 6 chr4 8336810 8341365 a 0 + 7 chr6 9024856 9028435 a 0 - 8 chr6 4856331 4856593 a 0 - 9 chr14 673553 676394 a 0 - 10 chr19 1631628 1635207 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfhiyiusr/f1.bed -b /tmp/tmpfhiyiusr/f2.bed Chromosome Start End Name Score Strand 0 chr1 5894320 5894577 a 0 + 1 chr2 5894320 5894577 a 0 + 2 chr2 5894320 5894577 a 0 + 3 chr2 5894320 5894577 a 0 + 4 chr2 5894320 5894577 a 0 + 5 chr2 5894320 5894577 a 0 + 6 chr2 5894320 5894577 a 0 + 7 chr2 5894320 5894577 a 0 + 8 chr2 5894320 5894577 a 0 + 9 chr2 5894320 5894577 a 0 + 10 chr2 5894320 5894577 a 0 - Chromosome Start End Name Score Strand 0 chr14 75422 77219 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpz95eiveh/f1.bed -b /tmp/tmpz95eiveh/f2.bed Chromosome Start End Name Score Strand 0 chr1 14080 17922 a 0 - Chromosome Start End Name Score Strand 0 chr1 1026 1098 a 0 + 1 chr1 459777 464324 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9rpvfyrt/f1.bed -b /tmp/tmp9rpvfyrt/f2.bed Chromosome Start End Name Score Strand 0 chr1 14080 17922 a 0 - Chromosome Start End Name Score Strand 0 chr1 1026 1098 a 0 + 1 chr1 459777 464324 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkxytf_3d/f1.bed -b /tmp/tmpkxytf_3d/f2.bed Chromosome Start End Name Score Strand 0 chr14 7203591 7205861 a 0 - 1 chr15 7794594 7799759 a 0 - 2 chrM 346788 353976 a 0 + Chromosome Start End Name Score Strand 0 chr1 7299449 7304468 a 0 + 1 chr1 1899324 1899371 a 0 - 2 chr1 2477407 2483505 a 0 - 3 chr1 2477407 2478595 a 0 - 4 chr1 9774674 9777597 a 0 - 5 chr1 1303448 1309898 a 0 - 6 chr1 3915966 3916955 a 0 - 7 chr17 5961227 5965531 a 0 + 8 chr18 8011755 8015411 a 0 + 9 chr18 1713833 1715105 a 0 + 10 chr19 6130943 6131932 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpy6pitorl/f1.bed -b /tmp/tmpy6pitorl/f2.bed Chromosome Start End Name Score Strand 0 chr1 4050654 4060653 a 0 + 1 chr1 4050654 4052843 a 0 + 2 chr3 7091687 7100899 a 0 - 3 chr7 5433359 5441904 a 0 + 4 chr10 1173048 1174045 a 0 - 5 chr15 4050654 4052092 a 0 + 6 chr16 4050654 4059199 a 0 + 7 chr20 7540675 7549220 a 0 + 8 chr20 4050654 4052874 a 0 - 9 chr22 4050654 4054289 a 0 - 10 chrX 4050654 4059070 a 0 + Chromosome Start End Name Score Strand 0 chr1 487728 495919 a 0 + 1 chr1 8463466 8466202 a 0 + 2 chr1 8463466 8472577 a 0 + 3 chr1 1166431 1173602 a 0 + 4 chr1 9199442 9207633 a 0 - 5 chr1 8463466 8465151 a 0 - 6 chr10 7880049 7882531 a 0 - 7 chr18 9432065 9432413 a 0 - 8 chrX 2015030 2019788 a 0 + 9 chrX 8463466 8471657 a 0 - cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpos961jn5/f1.bed -b /tmp/tmpos961jn5/f2.bed Chromosome Start End Name Score Strand 0 chr1 2871322 2873480 a 0 + 1 chr1 2886036 2892199 a 0 + 2 chr1 5256609 5262772 a 0 - 3 chr11 1379861 1385918 a 0 + 4 chr15 8041907 8048070 a 0 + 5 chr22 6850352 6855055 a 0 - Chromosome Start End Name Score Strand 0 chr1 2746790 2755687 a 0 + 1 chr1 3854287 3862207 a 0 + 2 chr1 9202836 9212479 a 0 - 3 chr1 3786110 3794413 a 0 - 4 chr1 4218856 4222701 a 0 - 5 chr1 4665886 4674869 a 0 - 6 chr1 4649859 4657378 a 0 - 7 chr1 2411599 2415309 a 0 - 8 chr13 1285584 1285947 a 0 + 9 chr16 7234607 7243021 a 0 + 10 chr16 9958228 9962118 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp9f8ijih9/f1.bed -b /tmp/tmp9f8ijih9/f2.bed Chromosome Start End Name Score Strand 0 chr1 8460806 8469070 a 0 + 1 chr1 7562566 7564056 a 0 + 2 chr1 7562566 7567836 a 0 + 3 chr2 3316944 3320018 a 0 - 4 chr14 9260132 9269363 a 0 + 5 chrX 6951216 6957283 a 0 - Chromosome Start End Name Score Strand 0 chr1 9018141 9025477 a 0 + 1 chr1 6692002 6698145 a 0 - 2 chr10 1881948 1890530 a 0 + 3 chr10 913870 914551 a 0 - 4 chrX 500808 506789 a 0 + 5 chrX 8141871 8150606 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpq8qzex49/f1.bed -b /tmp/tmpq8qzex49/f2.bed Chromosome Start End Name Score Strand 0 chr1 826432 832536 a 0 + 1 chr1 7618675 7621576 a 0 + 2 chr1 1933270 1938997 a 0 + 3 chr1 4586145 4588258 a 0 + 4 chr1 1718249 1724820 a 0 + 5 chr1 9359293 9368215 a 0 - 6 chr2 7439622 7439793 a 0 + 7 chr8 2684000 2692145 a 0 + 8 chr9 8699828 8701975 a 0 + 9 chr19 8301606 8310151 a 0 + 10 chr20 7951626 7961270 a 0 + Chromosome Start End Name Score Strand 0 chr1 3474438 3479529 a 0 + 1 chr1 4482357 4487448 a 0 + 2 chr1 4907752 4912843 a 0 + 3 chr1 1348210 1356849 a 0 + 4 chr1 3474438 3479621 a 0 + 5 chr10 3474438 3479529 a 0 + 6 chr17 3474438 3479529 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmppnnguwpu/f1.bed -b /tmp/tmppnnguwpu/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpb61jcxfp/f1.bed -b /tmp/tmpb61jcxfp/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqgzlq5m9/f1.bed -b /tmp/tmpqgzlq5m9/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpdz2rlwvf/f1.bed -b /tmp/tmpdz2rlwvf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpkl9rhuvf/f1.bed -b /tmp/tmpkl9rhuvf/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp_ec4i66o/f1.bed -b /tmp/tmp_ec4i66o/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpv67fbzs5/f1.bed -b /tmp/tmpv67fbzs5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpa5m6yvl4/f1.bed -b /tmp/tmpa5m6yvl4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpqb7vyg5d/f1.bed -b /tmp/tmpqb7vyg5d/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpnzb7jwst/f1.bed -b /tmp/tmpnzb7jwst/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpdyo0ke63/f1.bed -b /tmp/tmpdyo0ke63/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpj9rbdjha/f1.bed -b /tmp/tmpj9rbdjha/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpan4hv5zy/f1.bed -b /tmp/tmpan4hv5zy/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpwy1pdv46/f1.bed -b /tmp/tmpwy1pdv46/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmp0hhzl4rg/f1.bed -b /tmp/tmp0hhzl4rg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmpfqs36lvz/f1.bed -b /tmp/tmpfqs36lvz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -a /tmp/tmps7u83qo5/f1.bed -b /tmp/tmps7u83qo5/f2.bed _________________ test_k_nearest[upstream-True-opposite-last] __________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = True, strandedness = 'opposite' ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 514 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=True, E strandedness='opposite', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY3RkZBBmYGAEQwYIVs/Xmcjox/T0MANUFAwYAUooA6s=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqbvc4fvx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqbvc4fvx/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3z200wlt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3z200wlt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf5tf6oso/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5tf6oso/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz3hcl3d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz3hcl3d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9xudu_3_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xudu_3_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphsfupxm2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphsfupxm2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxafx7cu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxafx7cu5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuqio3q1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqio3q1j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpog0xcq69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpog0xcq69/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5lxozsab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5lxozsab/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp43h8h7fg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43h8h7fg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt5r5rejv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt5r5rejv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7dqtoj6r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dqtoj6r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphq5efvhh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphq5efvhh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptue2tluq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptue2tluq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqnzek0ut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqnzek0ut/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpla_9ofqr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpla_9ofqr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo6dkglze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo6dkglze/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0p7ji1lk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0p7ji1lk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplzvsbm_u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplzvsbm_u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_ps6i0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_ps6i0c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf51uzh08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf51uzh08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_knsym57/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_knsym57/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaoa769jt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaoa769jt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz8z5s_04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8z5s_04/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpayr5iz_c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpayr5iz_c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyk5b2zgm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyk5b2zgm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyw_zh95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyw_zh95/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppr3rg367/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppr3rg367/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2j48vibw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2j48vibw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb7xoa_fg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb7xoa_fg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6hszfrn4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6hszfrn4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpynaymlts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpynaymlts/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp841rppd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp841rppd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr8c83ot4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr8c83ot4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptpn9l_sq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpn9l_sq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2n0dkyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2n0dkyw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv13ym_rv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv13ym_rv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdsmvv3qq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdsmvv3qq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp462nfutb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp462nfutb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjf8x6g32/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjf8x6g32/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp10z1f6v8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp10z1f6v8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp08iiiclk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08iiiclk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps3_3hkwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3_3hkwj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9u53jt5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9u53jt5h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1vbbpaeq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vbbpaeq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq6wps7au/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6wps7au/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2r3kf9j4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2r3kf9j4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp18npo2rs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18npo2rs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0hvaeh5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0hvaeh5x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpti3pf21x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpti3pf21x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzdqrm_ck/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzdqrm_ck/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3t78x8e_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3t78x8e_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsy5b4s0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsy5b4s0p/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnxt7aeh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxt7aeh1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp049pmnlv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp049pmnlv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcgpb73zw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcgpb73zw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpegmnoyal/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegmnoyal/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr615i__c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr615i__c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ci_pxpd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ci_pxpd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0rignwfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rignwfa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2gj41w9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gj41w9l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsn0r_eq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsn0r_eq8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf1d9ba7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf1d9ba7e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppzf6r8nz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppzf6r8nz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpag5mshga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpag5mshga/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc30bp7du/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc30bp7du/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw5vmksdh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5vmksdh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ey6c5ns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ey6c5ns/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzk1743k1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzk1743k1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp34cvnrq6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp34cvnrq6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm9_s_b78/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9_s_b78/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl2hbl048/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl2hbl048/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2z5t8rdu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2z5t8rdu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps3dhlqze/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3dhlqze/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp08v0hg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp08v0hg9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptvi_6h9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvi_6h9l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoz335zj2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoz335zj2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpclyho5nj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpclyho5nj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3nhjbw1z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3nhjbw1z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpelhwtosj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpelhwtosj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1g1962zv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1g1962zv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnympvz4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnympvz4s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpl13yynei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl13yynei/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx8fmwvmg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8fmwvmg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyqbtw3_k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqbtw3_k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxjrk11ij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxjrk11ij/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfr3mk853/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfr3mk853/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8cjt129d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8cjt129d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd0o2fayh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0o2fayh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgzhguk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgzhguk3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwrxassh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwrxassh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmps2s8dmmo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps2s8dmmo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj1q6fb2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj1q6fb2c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkgcawu1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkgcawu1t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppxivjnm6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppxivjnm6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn_6h7r6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_6h7r6j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdii23e0y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdii23e0y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplai8h7c7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplai8h7c7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbf1vxf8y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbf1vxf8y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5izrd2vm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5izrd2vm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu56cu6m3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu56cu6m3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp8h4mkc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp8h4mkc8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuj_dgu0n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuj_dgu0n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz7g5t3w_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz7g5t3w_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3p4c2q_j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3p4c2q_j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmk66iy43/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmk66iy43/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzia8ikbe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzia8ikbe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzkmzofu1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzkmzofu1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8_kjay0m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_kjay0m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkxwxv2kl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkxwxv2kl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp54jmh7j1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54jmh7j1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbc192tzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbc192tzo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmm_tm15_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmm_tm15_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfzd9m_te/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfzd9m_te/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmph0ww7zey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph0ww7zey/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8k64en2v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8k64en2v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmprwuxg42a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprwuxg42a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppyqsxs_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppyqsxs_2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6vxijuu9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vxijuu9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68gytxnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68gytxnb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_afqgak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_afqgak/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1godrwlv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1godrwlv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfhywxvpv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfhywxvpv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj9pshvq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9pshvq8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcw9s0b4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcw9s0b4q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaiz2t21u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaiz2t21u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxgji9tps/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgji9tps/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmescplv4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmescplv4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpogtxjmkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogtxjmkk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwmnjs5h1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwmnjs5h1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyhtbnq7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyhtbnq7e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw8qa5b_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw8qa5b_2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp078knvln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp078knvln/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptf_zn0zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptf_zn0zj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxv_cd4g5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxv_cd4g5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw_v0kpb2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_v0kpb2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5pz1jbn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pz1jbn3/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr11 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain78-method_chain78] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________________ test_coverage[same] ______________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsxdjz4oq/f1.bed -b /tmp/tmpsxdjz4oq/f2.bed Chromosome Start End Name Score Strand 0 chr1 901315 909815 a 0 + 1 chr1 9281602 9289961 a 0 - 2 chr1 6823239 6828397 a 0 - 3 chr1 6338035 6347118 a 0 - 4 chr7 1253852 1255507 a 0 + 5 chrX 991392 996184 a 0 - Chromosome Start End Name Score Strand 0 chr1 7178279 7185236 a 0 + 1 chr1 7992106 7998116 a 0 + 2 chr1 159606 163600 a 0 - 3 chr1 6573309 6577101 a 0 - 4 chr1 4066197 4066527 a 0 - 5 chr2 1461150 1463146 a 0 + 6 chr7 5347048 5355567 a 0 + 7 chr8 2870947 2874331 a 0 - 8 chr11 3794567 3800304 a 0 + 9 chr17 2859240 2860576 a 0 - 10 chr19 7377572 7383241 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1sftnxy2/f1.bed -b /tmp/tmp1sftnxy2/f2.bed Chromosome Start End Name Score Strand 0 chr1 1671649 1675596 a 0 - 1 chr18 10000000 10006281 a 0 - 2 chrM 8854189 8857486 a 0 - Chromosome Start End Name Score Strand 0 chr1 8703329 8704881 a 0 + 1 chr3 6516392 6522745 a 0 + 2 chr11 6759337 6765287 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmprbmekq1m/f1.bed -b /tmp/tmprbmekq1m/f2.bed Chromosome Start End Name Score Strand 0 chr1 66305 68124 a 0 + 1 chr1 721153 722972 a 0 + 2 chr18 10000000 10000258 a 0 + 3 chrM 66305 68124 a 0 + Chromosome Start End Name Score Strand 0 chr1 9414658 9416196 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpty7nx6_4/f1.bed -b /tmp/tmpty7nx6_4/f2.bed Chromosome Start End Name Score Strand 0 chr1 7601193 7602174 a 0 + Chromosome Start End Name Score Strand 0 chr1 6292530 6298803 a 0 + 1 chr1 3675500 3681773 a 0 - 2 chr5 3959000 3965273 a 0 + 3 chr5 3517876 3526004 a 0 - 4 chr15 2009470 2015743 a 0 - 5 chr17 8435966 8442239 a 0 + 6 chr19 1 9662 a 0 - 7 chr20 7872380 7878653 a 0 + 8 chr22 8429043 8435316 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp0fcqec8p/f1.bed -b /tmp/tmp0fcqec8p/f2.bed Chromosome Start End Name Score Strand 0 chr1 4868213 4874342 a 0 - 1 chr1 1993092 2000759 a 0 - 2 chr1 6999773 7006698 a 0 - 3 chr1 7231806 7241487 a 0 - 4 chr1 6233970 6238556 a 0 - 5 chr1 4711016 4716945 a 0 - 6 chr10 8229197 8238074 a 0 - 7 chr12 1842509 1847006 a 0 + 8 chr14 9794449 9795298 a 0 + 9 chr14 7245601 7250597 a 0 + 10 chr18 6153492 6159615 a 0 + Chromosome Start End Name Score Strand 0 chr1 6871622 6881621 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmphiphu06c/f1.bed -b /tmp/tmphiphu06c/f2.bed Chromosome Start End Name Score Strand 0 chr1 6871622 6881621 a 0 + Chromosome Start End Name Score Strand 0 chr1 6871622 6881621 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp8h5xeoh_/f1.bed -b /tmp/tmp8h5xeoh_/f2.bed Chromosome Start End Name Score Strand 0 chr1 1740510 1747733 a 0 - 1 chr1 3963832 3971055 a 0 - 2 chr1 3963832 3964701 a 0 - 3 chr1 4728546 4735256 a 0 - 4 chr1 1765039 1772262 a 0 - 5 chr1 9728935 9732747 a 0 - 6 chr10 3963832 3971055 a 0 - 7 chr11 4671341 4678564 a 0 - 8 chr16 2620060 2626380 a 0 - 9 chr21 3963832 3971055 a 0 - 10 chrX 2189942 2192568 a 0 - Chromosome Start End Name Score Strand 0 chr1 57658 67657 a 0 + 1 chr1 7122916 7132915 a 0 - 2 chr1 6123118 6133117 a 0 - 3 chr1 9989354 9999353 a 0 - 4 chr1 1972644 1982643 a 0 - 5 chr1 9342651 9352650 a 0 - 6 chr1 3943651 3953650 a 0 - 7 chr4 5447492 5457491 a 0 + 8 chr9 4035892 4045891 a 0 - 9 chr10 1458226 1468225 a 0 + 10 chr15 3897853 3907852 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp26p1sgg1/f1.bed -b /tmp/tmp26p1sgg1/f2.bed Chromosome Start End Name Score Strand 0 chr1 8243165 8251360 a 0 + 1 chr1 8520226 8523608 a 0 + 2 chr1 6339819 6341383 a 0 - 3 chr1 9942542 9951753 a 0 - 4 chr1 7384084 7387780 a 0 - 5 chr7 94889 104444 a 0 + 6 chr8 7371942 7380882 a 0 - 7 chr9 6767710 6772213 a 0 - 8 chr20 3584395 3590340 a 0 + 9 chr22 4412101 4412102 a 0 - 10 chr22 5790781 5798132 a 0 - Chromosome Start End Name Score Strand 0 chr1 9999999 10001669 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa2e4juqx/f1.bed -b /tmp/tmpa2e4juqx/f2.bed Chromosome Start End Name Score Strand 0 chr1 6152800 6153931 a 0 + 1 chr4 6152800 6160220 a 0 + 2 chr14 6152800 6155984 a 0 + 3 chr18 6152800 6157436 a 0 - 4 chrY 7408290 7408297 a 0 + Chromosome Start End Name Score Strand 0 chr1 8601080 8606886 a 0 + 1 chr1 4402230 4409066 a 0 - 2 chr1 6531728 6541336 a 0 - 3 chr6 8601080 8606886 a 0 + 4 chr6 845877 854114 a 0 + 5 chr15 9297190 9304043 a 0 - 6 chr18 9072222 9078389 a 0 - cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpud3u48sl/f1.bed -b /tmp/tmpud3u48sl/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpsixm8qt4/f1.bed -b /tmp/tmpsixm8qt4/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp3gfs0afd/f1.bed -b /tmp/tmp3gfs0afd/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpaj47ate6/f1.bed -b /tmp/tmpaj47ate6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpofv_272l/f1.bed -b /tmp/tmpofv_272l/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpq67vr1_3/f1.bed -b /tmp/tmpq67vr1_3/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpub8oyh7t/f1.bed -b /tmp/tmpub8oyh7t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjfwclp64/f1.bed -b /tmp/tmpjfwclp64/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpa5x5d0ds/f1.bed -b /tmp/tmpa5x5d0ds/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpvz6a_9s8/f1.bed -b /tmp/tmpvz6a_9s8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpc7c1vayo/f1.bed -b /tmp/tmpc7c1vayo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpjie6sy1t/f1.bed -b /tmp/tmpjie6sy1t/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpwb05hyks/f1.bed -b /tmp/tmpwb05hyks/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpr4oaez5i/f1.bed -b /tmp/tmpr4oaez5i/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmp1rav7c5g/f1.bed -b /tmp/tmp1rav7c5g/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpmqs5zzx7/f1.bed -b /tmp/tmpmqs5zzx7/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -s -a /tmp/tmpy1u65_9k/f1.bed -b /tmp/tmpy1u65_9k/f2.bed __________ test_three_in_a_row[strandedness_chain124-method_chain124] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________________ test_coverage[opposite] ____________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", strandedness) tests/test_binary.py:207: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:238: in test_coverage result = gr.coverage(gr2, strandedness=strandedness) pyranges/pyranges.py:1341: in coverage other = other.merge(count=True, strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_coverage( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0ynus0o0/f1.bed -b /tmp/tmp0ynus0o0/f2.bed Chromosome Start End Name Score Strand 0 chr1 2500398 2500785 a 0 + 1 chr1 5850455 5852459 a 0 - 2 chr1 1236289 1243756 a 0 - 3 chr1 2011057 2014517 a 0 - 4 chr3 9772536 9780083 a 0 + 5 chr15 4312375 4312820 a 0 + Chromosome Start End Name Score Strand 0 chr1 8003700 8013699 a 0 + 1 chr1 8536065 8540184 a 0 + 2 chr1 2546100 2555234 a 0 + 3 chr1 266166 269101 a 0 - 4 chr1 9222813 9224961 a 0 - 5 chr1 8657575 8667575 a 0 - 6 chr1 1 2 a 0 - 7 chr1 3019863 3023299 a 0 - 8 chr15 287118 297114 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp0ppgd0ux/f1.bed -b /tmp/tmp0ppgd0ux/f2.bed Chromosome Start End Name Score Strand 0 chr1 8003700 8013699 a 0 + 1 chr1 8536065 8540184 a 0 + 2 chr1 2546100 2555234 a 0 + 3 chr1 266166 269101 a 0 - 4 chr1 9222813 9224961 a 0 - 5 chr1 8657575 8667575 a 0 - 6 chr1 1 2 a 0 - 7 chr1 3019863 3023299 a 0 - 8 chr15 287118 297114 a 0 - Chromosome Start End Name Score Strand 0 chr1 8003700 8013699 a 0 + 1 chr1 8536065 8540184 a 0 + 2 chr1 2546100 2555234 a 0 + 3 chr1 266166 269101 a 0 - 4 chr1 9222813 9224961 a 0 - 5 chr1 8657575 8667575 a 0 - 6 chr1 1 2 a 0 - 7 chr1 3019863 3023299 a 0 - 8 chr15 287118 297114 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp04fddhl7/f1.bed -b /tmp/tmp04fddhl7/f2.bed Chromosome Start End Name Score Strand 0 chr1 65824 66085 a 0 + 1 chr1 65824 69154 a 0 + 2 chr1 65824 66085 a 0 + 3 chr1 65824 66085 a 0 + 4 chr1 65824 66085 a 0 - 5 chr1 853809 854070 a 0 - 6 chr1 1048838 1049099 a 0 - 7 chr2 723469 723730 a 0 - Chromosome Start End Name Score Strand 0 chr1 66312 66889 a 0 - 1 chr5 66088 66358 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp_h2ydzyu/f1.bed -b /tmp/tmp_h2ydzyu/f2.bed Chromosome Start End Name Score Strand 0 chr1 66312 66889 a 0 - 1 chr5 66088 66358 a 0 - Chromosome Start End Name Score Strand 0 chr1 66312 66889 a 0 - 1 chr5 66088 66358 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpa6g1e23d/f1.bed -b /tmp/tmpa6g1e23d/f2.bed Chromosome Start End Name Score Strand 0 chr5 65793 66050 a 0 - Chromosome Start End Name Score Strand 0 chr1 66312 66582 a 0 + 1 chr1 66088 69674 a 0 + 2 chr1 65571 68410 a 0 + 3 chr1 65571 68410 a 0 + 4 chr1 65571 68410 a 0 + 5 chr1 65571 68410 a 0 - 6 chr1 65571 68410 a 0 - 7 chr1 65571 68410 a 0 - 8 chr1 65571 65842 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpc7m8rf8k/f1.bed -b /tmp/tmpc7m8rf8k/f2.bed Chromosome Start End Name Score Strand 0 chr1 66312 66582 a 0 + 1 chr1 66088 69674 a 0 + 2 chr1 65571 68410 a 0 + 3 chr1 65571 68410 a 0 + 4 chr1 65571 68410 a 0 + 5 chr1 65571 68410 a 0 - 6 chr1 65571 68410 a 0 - 7 chr1 65571 68410 a 0 - 8 chr1 65571 65842 a 0 - Chromosome Start End Name Score Strand 0 chr1 66312 66582 a 0 + 1 chr1 66088 69674 a 0 + 2 chr1 65571 68410 a 0 + 3 chr1 65571 68410 a 0 + 4 chr1 65571 68410 a 0 + 5 chr1 65571 68410 a 0 - 6 chr1 65571 68410 a 0 - 7 chr1 65571 68410 a 0 - 8 chr1 65571 65842 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4dbbv5yu/f1.bed -b /tmp/tmp4dbbv5yu/f2.bed Chromosome Start End Name Score Strand 0 chr22 2150171 2156508 a 0 - Chromosome Start End Name Score Strand 0 chr1 4576999 4583629 a 0 + 1 chr1 7884411 7894215 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp9tus2xk8/f1.bed -b /tmp/tmp9tus2xk8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1563266 1563330 a 0 + 1 chr19 5119313 5123363 a 0 + 2 chr19 8482956 8484031 a 0 + 3 chrM 4384319 4393090 a 0 + Chromosome Start End Name Score Strand 0 chr19 798086 807945 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpqesauniq/f1.bed -b /tmp/tmpqesauniq/f2.bed Chromosome Start End Name Score Strand 0 chr1 6051674 6052547 a 0 + 1 chr1 9999999 10007926 a 0 + 2 chr1 7679161 7680860 a 0 + 3 chr1 9602360 9607728 a 0 + 4 chr1 3969050 3969382 a 0 + 5 chr1 1895298 1898187 a 0 - 6 chr1 3013932 3018579 a 0 - 7 chr1 5924980 5930050 a 0 - 8 chr1 1368116 1371956 a 0 - 9 chr7 5646516 5650356 a 0 + 10 chr16 2 7990 a 0 + Chromosome Start End Name Score Strand 0 chr1 8243383 8244676 a 0 + 1 chr1 6472722 6477082 a 0 + 2 chr1 711673 720443 a 0 + 3 chr1 1619710 1621504 a 0 - 4 chr1 2680903 2680905 a 0 - 5 chr1 4425517 4427456 a 0 - 6 chr1 9436879 9445264 a 0 - 7 chr1 9344946 9352405 a 0 - 8 chr1 3832772 3842527 a 0 - 9 chr1 6846579 6854724 a 0 - 10 chr7 8639024 8643863 a 0 - cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmptqfyqlsc/f1.bed -b /tmp/tmptqfyqlsc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpf0iio2_6/f1.bed -b /tmp/tmpf0iio2_6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpxwf17foc/f1.bed -b /tmp/tmpxwf17foc/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpadhg7a_6/f1.bed -b /tmp/tmpadhg7a_6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpdsecsrat/f1.bed -b /tmp/tmpdsecsrat/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpb0b5d6p8/f1.bed -b /tmp/tmpb0b5d6p8/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4kc4gtve/f1.bed -b /tmp/tmp4kc4gtve/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpg2val2l5/f1.bed -b /tmp/tmpg2val2l5/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp1uuwbn_n/f1.bed -b /tmp/tmp1uuwbn_n/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpak3aq2wo/f1.bed -b /tmp/tmpak3aq2wo/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpzdrdh2pi/f1.bed -b /tmp/tmpzdrdh2pi/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpwfnfd6kg/f1.bed -b /tmp/tmpwfnfd6kg/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp4s_lynpz/f1.bed -b /tmp/tmp4s_lynpz/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpjbuyzpu6/f1.bed -b /tmp/tmpjbuyzpu6/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpe5mf64sr/f1.bed -b /tmp/tmpe5mf64sr/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmpovr6z3td/f1.bed -b /tmp/tmpovr6z3td/f2.bed Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + Chromosome Start End Name Score Strand 0 chr1 1 2 a 0 + cmd cmd cmd cmd cmd bedtools coverage -S -a /tmp/tmp2shp39_u/f1.bed -b /tmp/tmp2shp39_u/f2.bed ___________________ test_k_nearest[upstream-True-same-last] ____________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=True, E strandedness='same', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwojf58fw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwojf58fw/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc3do0vmy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc3do0vmy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp940fqsh4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp940fqsh4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ewqintj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ewqintj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3oixk4is/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3oixk4is/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxeantmw5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxeantmw5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdi0ju3wd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdi0ju3wd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9bk3drom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9bk3drom/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwk1cedei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwk1cedei/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw4j690dq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4j690dq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1kqhovw6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1kqhovw6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp43ny6ppz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43ny6ppz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4eof_oij/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4eof_oij/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplu747g5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplu747g5a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe18ei7vc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe18ei7vc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp74x6t81/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp74x6t81/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ckgfh91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ckgfh91/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjwp_d8km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjwp_d8km/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz2xn5k96/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz2xn5k96/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmplh40_pbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplh40_pbh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpakxfhfxg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpakxfhfxg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu9m_6tcb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu9m_6tcb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmv9jbsu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmv9jbsu7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3fr19hs0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3fr19hs0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxh0f6rue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxh0f6rue/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxqpnx4mp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqpnx4mp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybv2ncq7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybv2ncq7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpju5rb7vf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpju5rb7vf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpybdakvcv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpybdakvcv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2vlgzdp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vlgzdp0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbo1t7v2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo1t7v2c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_cd7807n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cd7807n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpu6cv5zqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu6cv5zqj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpoyn4958g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoyn4958g/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxdhwxtor/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxdhwxtor/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphlo7ucwa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlo7ucwa/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwql6t5jp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwql6t5jp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5gbi4o_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gbi4o_n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr0s1mp08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0s1mp08/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn9o7psik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9o7psik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqcnqmkht/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqcnqmkht/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0opys3w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0opys3w8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv5ct4u9_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5ct4u9_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_1aj8qbw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1aj8qbw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvs_uqln6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvs_uqln6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_7imv4ue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7imv4ue/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxl6vkyl0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxl6vkyl0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7s91f2t0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s91f2t0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv0ts8ezj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv0ts8ezj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp965mxj0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp965mxj0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5nf009o1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nf009o1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9x1phsk5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9x1phsk5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd7cmr7y_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7cmr7y_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuz5d1mqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuz5d1mqg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp91mdwnyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91mdwnyu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk3zu5811/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3zu5811/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt4xhvavn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4xhvavn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjhwr_9ey/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhwr_9ey/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgfp41twe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgfp41twe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1_84dfp7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1_84dfp7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_3nf8ydb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_3nf8ydb/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr14 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________________ test_subtraction[same] ____________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpv1pn2o5j/f1.bed -b /tmp/tmpv1pn2o5j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp4mdwiv3q/f1.bed -b /tmp/tmp4mdwiv3q/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpazuu_dks/f1.bed -b /tmp/tmpazuu_dks/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp1u7g7yfb/f1.bed -b /tmp/tmp1u7g7yfb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpcm4nlzat/f1.bed -b /tmp/tmpcm4nlzat/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpumfy02js/f1.bed -b /tmp/tmpumfy02js/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxswjsjll/f1.bed -b /tmp/tmpxswjsjll/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpsuzkyfhn/f1.bed -b /tmp/tmpsuzkyfhn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpzvdt09l_/f1.bed -b /tmp/tmpzvdt09l_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt7tz865h/f1.bed -b /tmp/tmpt7tz865h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt0oa8mm9/f1.bed -b /tmp/tmpt0oa8mm9/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpuo75tav0/f1.bed -b /tmp/tmpuo75tav0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpj8at0zz2/f1.bed -b /tmp/tmpj8at0zz2/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp7hs46h7m/f1.bed -b /tmp/tmp7hs46h7m/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt05w5aza/f1.bed -b /tmp/tmpt05w5aza/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpkj45uwlp/f1.bed -b /tmp/tmpkj45uwlp/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpi0ypy026/f1.bed -b /tmp/tmpi0ypy026/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpt1dek20n/f1.bed -b /tmp/tmpt1dek20n/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpoe9yhyve/f1.bed -b /tmp/tmpoe9yhyve/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp8p4odn_o/f1.bed -b /tmp/tmp8p4odn_o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp23u_bs8u/f1.bed -b /tmp/tmp23u_bs8u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpvjvvm9rs/f1.bed -b /tmp/tmpvjvvm9rs/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpls2k_z1h/f1.bed -b /tmp/tmpls2k_z1h/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpxg2_x29w/f1.bed -b /tmp/tmpxg2_x29w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmpds26tb65/f1.bed -b /tmp/tmpds26tb65/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -s -a /tmp/tmp3pdmd8um/f1.bed -b /tmp/tmp3pdmd8um/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting __________ test_three_in_a_row[strandedness_chain125-method_chain125] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2723592 | 2726666 | a | 0 | + | E | chr1 | 66613 | 71152 | a | 0 | - | E | chr1 | 66562 | 66822 | a | 0 | - | E | chr1 | 66613 | 71152 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66050 | 66308 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY6w8t/f+x4U3JDN/sDOo2fBuYmNkZBKOZGJktP3aw8DKyACEzIzMBevnh2r2swOZQMTCCATMDDqMLCaMzMw8QA5QDYOa4C6gQgaQ8nAGRrBGIGRgZAISID6IAJMMDABlVg8B') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________________________ test_subtraction[opposite] __________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpi3s629cj/f1.bed -b /tmp/tmpi3s629cj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpwmj5dh1y/f1.bed -b /tmp/tmpwmj5dh1y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpla00r48j/f1.bed -b /tmp/tmpla00r48j/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_vq8huzn/f1.bed -b /tmp/tmp_vq8huzn/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc5ro8xdh/f1.bed -b /tmp/tmpc5ro8xdh/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpgh2l2uuq/f1.bed -b /tmp/tmpgh2l2uuq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp7zqzckk1/f1.bed -b /tmp/tmp7zqzckk1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnbt_ieog/f1.bed -b /tmp/tmpnbt_ieog/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpkqxtn9bg/f1.bed -b /tmp/tmpkqxtn9bg/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpfu14zhrv/f1.bed -b /tmp/tmpfu14zhrv/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpqrev99uf/f1.bed -b /tmp/tmpqrev99uf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpc91azqrm/f1.bed -b /tmp/tmpc91azqrm/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp8h3wqja6/f1.bed -b /tmp/tmp8h3wqja6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvbhsuvy1/f1.bed -b /tmp/tmpvbhsuvy1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpvyvlesn3/f1.bed -b /tmp/tmpvyvlesn3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpnto690mj/f1.bed -b /tmp/tmpnto690mj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpm3267jgj/f1.bed -b /tmp/tmpm3267jgj/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmped7qpjab/f1.bed -b /tmp/tmped7qpjab/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpbxyomyq3/f1.bed -b /tmp/tmpbxyomyq3/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzn_gs34d/f1.bed -b /tmp/tmpzn_gs34d/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_xsxwbnx/f1.bed -b /tmp/tmp_xsxwbnx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpzfjtf4oa/f1.bed -b /tmp/tmpzfjtf4oa/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp0gqckuxx/f1.bed -b /tmp/tmp0gqckuxx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmplne3lg_6/f1.bed -b /tmp/tmplne3lg_6/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmp_fe29_gd/f1.bed -b /tmp/tmp_fe29_gd/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -S -a /tmp/tmpsa_znra5/f1.bed -b /tmp/tmpsa_znra5/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting ___________________ test_k_nearest[upstream-True-False-last] ___________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = True, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:115: in nearest_previous lidx, ridx, dist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=True, E strandedness=False, E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmph6oe4cek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph6oe4cek/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3mpboxwp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3mpboxwp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg0z623xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg0z623xp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp31pqcom4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31pqcom4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1aqesm00/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1aqesm00/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp68wc0q9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp68wc0q9w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpglgdpdat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpglgdpdat/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg8tl22b_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8tl22b_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwcbqz75t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwcbqz75t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqm6cvdsn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqm6cvdsn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6o1vk4k5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o1vk4k5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpd_jm16tg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd_jm16tg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt04im021/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt04im021/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy58bn7ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy58bn7ua/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo67axjm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo67axjm5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmtgfhuau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmtgfhuau/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgy5whypp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy5whypp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwkj0_dyb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwkj0_dyb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7l5ieab9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7l5ieab9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvi5usnsy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvi5usnsy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwv9nk_zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwv9nk_zc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpango1u62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpango1u62/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxvkomele/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvkomele/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpv24alaa6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv24alaa6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp43fs_rth/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43fs_rth/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpctfiro9n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpctfiro9n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpil_lp_06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpil_lp_06/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwqcr3k0v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqcr3k0v/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2f6shvs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2f6shvs5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgbet75cx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbet75cx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnwoo58tm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwoo58tm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj5702ugu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5702ugu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpq2kz0iou/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2kz0iou/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3r7y1br_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3r7y1br_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp37qqzzt2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37qqzzt2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmppw65z38f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppw65z38f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpohyoc9v4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohyoc9v4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphunnz_yf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphunnz_yf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3w4ce43l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3w4ce43l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2a5gsmkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2a5gsmkm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5pg3j8hk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pg3j8hk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpznx5kp49/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpznx5kp49/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa4zmwjby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4zmwjby/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi38hy8n3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi38hy8n3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp25rhjqph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25rhjqph/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp6jkcniz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp6jkcniz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcenmvti4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcenmvti4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1j7f6s2f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1j7f6s2f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9ty53m01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ty53m01/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_rtifjrs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_rtifjrs/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi6r7m10k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi6r7m10k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa_0t68s_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa_0t68s_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsn85li37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsn85li37/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2d7cgpkv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d7cgpkv/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgk95onnb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgk95onnb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbqyi73ch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqyi73ch/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpn0cuteak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn0cuteak/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6p89se7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6p89se7l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -id -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphz0ry921/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphz0ry921/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrM than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr13 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr3 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________________________ test_subtraction[False] ____________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness", ["same", "opposite", False]) # tests/test_binary.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:308: in test_subtraction result = gr.subtract(gr2, strandedness=strandedness) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_subtraction( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv_t5z01o/f1.bed -b /tmp/tmpv_t5z01o/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmphw297dg0/f1.bed -b /tmp/tmphw297dg0/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpy8zquryw/f1.bed -b /tmp/tmpy8zquryw/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpv4u_gxof/f1.bed -b /tmp/tmpv4u_gxof/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2n1zrhq7/f1.bed -b /tmp/tmp2n1zrhq7/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu2ocwnz_/f1.bed -b /tmp/tmpu2ocwnz_/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpo11_7wtf/f1.bed -b /tmp/tmpo11_7wtf/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp6e30n8fb/f1.bed -b /tmp/tmp6e30n8fb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpu9kzz3bz/f1.bed -b /tmp/tmpu9kzz3bz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpau3e5c_w/f1.bed -b /tmp/tmpau3e5c_w/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpazdbu4os/f1.bed -b /tmp/tmpazdbu4os/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpt9q14rka/f1.bed -b /tmp/tmpt9q14rka/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpi6trz2gx/f1.bed -b /tmp/tmpi6trz2gx/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp02dorr5u/f1.bed -b /tmp/tmp02dorr5u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp2e3rikde/f1.bed -b /tmp/tmp2e3rikde/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpbw8kqwc8/f1.bed -b /tmp/tmpbw8kqwc8/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp32rhrgc1/f1.bed -b /tmp/tmp32rhrgc1/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpdtiyunda/f1.bed -b /tmp/tmpdtiyunda/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpl0zlghg4/f1.bed -b /tmp/tmpl0zlghg4/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpravc7f_u/f1.bed -b /tmp/tmpravc7f_u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmptifvsdlz/f1.bed -b /tmp/tmptifvsdlz/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmposmf4t1y/f1.bed -b /tmp/tmposmf4t1y/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpw9cj69nr/f1.bed -b /tmp/tmpw9cj69nr/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpiyqy3sdq/f1.bed -b /tmp/tmpiyqy3sdq/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmpprqkwwcb/f1.bed -b /tmp/tmpprqkwwcb/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting cmd cmd cmd cmd cmd bedtools subtract -a /tmp/tmp092bmg8u/f1.bed -b /tmp/tmp092bmg8u/f2.bed subtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtractingsubtracting __________ test_three_in_a_row[strandedness_chain126-method_chain126] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ___________________ test_k_nearest[None-False-opposite-last] ___________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = False, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 258 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 65539 | a | 0 | - | E | chr1 | 65537 | 65539 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=False, E strandedness='opposite', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RgZKhnQABGMGaM4mXMz5XpB7MZoRKMADZsAnk=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmphlo_0tgz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlo_0tgz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6ke04ch3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ke04ch3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7qgluccg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qgluccg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpb82mhmwv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb82mhmwv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppwo23fm0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwo23fm0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4ywi_z04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ywi_z04/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk886xsl5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk886xsl5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0m11fki9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0m11fki9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9ax2ll6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9ax2ll6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpte7xq0eo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpte7xq0eo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaq5wikp2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq5wikp2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw4qgwhh1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw4qgwhh1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4cc6f5vy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cc6f5vy/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1n8uh1_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1n8uh1_e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgsfpab4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgsfpab4y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpadcod7gd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadcod7gd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp07l38k8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp07l38k8_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpifjrj1yf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifjrj1yf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpja_sdnhv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpja_sdnhv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp10bokp1h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp10bokp1h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdjkbm7nh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdjkbm7nh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplk8hpu9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplk8hpu9c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpga9weu3k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpga9weu3k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg3ykiyeu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3ykiyeu/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9m8xor8r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9m8xor8r/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp572zgm6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp572zgm6w/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpumbiljb8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpumbiljb8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppo83eh_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppo83eh_5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsgf2lwow/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgf2lwow/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0b5n_6rs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0b5n_6rs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmppwuoks86/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppwuoks86/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsm28yob7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsm28yob7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnkbzij4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnkbzij4y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqujglc9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqujglc9f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7mg_fhj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mg_fhj3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8swcg06m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8swcg06m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6wzox_w6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wzox_w6/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfwssuwg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfwssuwg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdy4kxr3c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdy4kxr3c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx278ib9y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx278ib9y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkq6ckmuj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkq6ckmuj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuf3rgor0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuf3rgor0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg7nsba16/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7nsba16/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx9pq4qe5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9pq4qe5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmptsf0rg24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptsf0rg24/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5m5frfd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5m5frfd7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp123b7trb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp123b7trb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxu02etn1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxu02etn1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpirm481fh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpirm481fh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdm_k95n5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdm_k95n5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwkg8hdur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwkg8hdur/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6sanl0fe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6sanl0fe/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrY than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________________ test_nearest[None-True-False] _________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = True, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=True, E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_6z1f3w8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6z1f3w8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgnrazn6a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgnrazn6a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf0u7lf2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0u7lf2t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu8xd5bk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8xd5bk3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_bns611d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_bns611d/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 71527 73096 + 0 1 chr1 871971 873462 - 0 2 chr1 5536835 5538404 - 0 3 chr1 6530364 6531933 - 0 4 chr1 7985675 7993180 - 0 5 chr1 9247714 9252837 - 0 6 chr1 9999999 10001568 + 0 7 chr13 1769551 1771120 + 0 8 chr21 8412490 8415960 + 0 9 chr5 3680958 3686917 + 0 10 chr8 3672673 3675278 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9999999 | 10001568 | a | 0 | ... | | chr1 | 71527 | 73096 | a | 0 | ... | | chr1 | 7985675 | 7993180 | a | 0 | ... | | chr1 | 6530364 | 6531933 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr5 | 3680958 | 3686917 | a | 0 | ... | | chr8 | 3672673 | 3675278 | a | 0 | ... | | chr13 | 1769551 | 1771120 | a | 0 | ... | | chr21 | 8412490 | 8415960 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 71527 73096 + 0 4 chr1 871971 873462 - 0 9 chr13 1769551 1771120 + 0 8 chr8 3672673 3675278 - 0 7 chr5 3680958 3686917 + 0 6 chr1 5536835 5538404 - 0 3 chr1 6530364 6531933 - 0 2 chr1 7985675 7993180 - 0 10 chr21 8412490 8415960 + 0 5 chr1 9247714 9252837 - 0 0 chr1 9999999 10001568 + 0 df2 Chromosome Start End Strand Distance 0 chr1 71527 73096 + 0 1 chr1 871971 873462 - 0 7 chr13 1769551 1771120 + 0 10 chr8 3672673 3675278 - 0 9 chr5 3680958 3686917 + 0 2 chr1 5536835 5538404 - 0 3 chr1 6530364 6531933 - 0 4 chr1 7985675 7993180 - 0 8 chr21 8412490 8415960 + 0 5 chr1 9247714 9252837 - 0 6 chr1 9999999 10001568 + 0 Actual Chromosome Start End Strand Distance 0 chr1 71527 73096 + 0 1 chr1 871971 873462 - 0 2 chr1 5536835 5538404 - 0 3 chr1 6530364 6531933 - 0 4 chr1 7985675 7993180 - 0 5 chr1 9247714 9252837 - 0 6 chr1 9999999 10001568 + 0 7 chr13 1769551 1771120 + 0 8 chr21 8412490 8415960 + 0 9 chr5 3680958 3686917 + 0 10 chr8 3672673 3675278 - 0 Expected Chromosome Start End Strand Distance 0 chr1 71527 73096 + 0 1 chr1 871971 873462 - 0 2 chr1 5536835 5538404 - 0 3 chr1 6530364 6531933 - 0 4 chr1 7985675 7993180 - 0 5 chr1 9247714 9252837 - 0 6 chr1 9999999 10001568 + 0 7 chr13 1769551 1771120 + 0 8 chr21 8412490 8415960 + 0 9 chr5 3680958 3686917 + 0 10 chr8 3672673 3675278 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqqp39208/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqqp39208/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofk1h7d4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofk1h7d4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1n35t_og/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1n35t_og/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmiaplx1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmiaplx1s/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 9353 - 0 1 chr1 7374913 7380140 + 0 2 chr20 6100393 6106099 + 0 3 chr21 1277238 1286973 - 0 4 chr7 824410 832381 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 7374913 | 7380140 | a | 0 | ... | | chr1 | 2 | 9353 | a | 0 | ... | | chr7 | 824410 | 832381 | a | 0 | ... | | chr20 | 6100393 | 6106099 | a | 0 | ... | | chr21 | 1277238 | 1286973 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 2 9353 - 0 2 chr7 824410 832381 - 0 4 chr21 1277238 1286973 - 0 3 chr20 6100393 6106099 + 0 0 chr1 7374913 7380140 + 0 df2 Chromosome Start End Strand Distance 0 chr1 2 9353 - 0 4 chr7 824410 832381 - 0 3 chr21 1277238 1286973 - 0 2 chr20 6100393 6106099 + 0 1 chr1 7374913 7380140 + 0 Actual Chromosome Start End Strand Distance 0 chr1 2 9353 - 0 1 chr1 7374913 7380140 + 0 2 chr20 6100393 6106099 + 0 3 chr21 1277238 1286973 - 0 4 chr7 824410 832381 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 9353 - 0 1 chr1 7374913 7380140 + 0 2 chr20 6100393 6106099 + 0 3 chr21 1277238 1286973 - 0 4 chr7 824410 832381 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphcvonzig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphcvonzig/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00rx2w95/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00rx2w95/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa6l89u0d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa6l89u0d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt8qw44mp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt8qw44mp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphv1z7xqn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphv1z7xqn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz0g6rmxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0g6rmxr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsaskr6g3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsaskr6g3/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpebp9991p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebp9991p/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5z01t1dc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5z01t1dc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zqh_914/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zqh_914/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe00okm66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe00okm66/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpatgda7l_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpatgda7l_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_y9dywsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_y9dywsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsazxi82y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsazxi82y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb3mz6yly/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3mz6yly/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3qqokjq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3qqokjq8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6mavt8tn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6mavt8tn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf9ndagwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9ndagwj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcno6yx6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcno6yx6o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp989s661b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp989s661b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqxstpxef/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqxstpxef/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmproc9c0_w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmproc9c0_w/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain127-method_chain127] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr4 | 1573122 | 1573635 | a | 0 | + | E | chr4 | 1114369 | 1114882 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 69122 | 69379 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicFYnBDQAQFMVeCW4SB4kdrOJmHMt7v6empVU2hSeTgYHQWSCRIso6iRUnsktH16oPRDcBxg==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain82-method_chain82] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BgYTQ889CMAQgYGRiQKDAAADW6Ahw=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_k_nearest[None-False-same-last] _____________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = False, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=False, E strandedness='same', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwredqe4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwredqe4z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmputpk0lr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputpk0lr3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp49li8jmt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp49li8jmt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmzsza3w5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmzsza3w5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsyqkrgbf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyqkrgbf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzky4t_im/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzky4t_im/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpqdintxgg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqdintxgg/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpg57w3emk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg57w3emk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3d3kuz5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3d3kuz5_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0d23x5vx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0d23x5vx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgx8dn86k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgx8dn86k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgdesbof1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdesbof1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt1kmq_1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1kmq_1j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9jrtmopt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jrtmopt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpr19yuv5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr19yuv5x/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplqaykl5h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplqaykl5h/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpktq4xscd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpktq4xscd/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp33rm6c9a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33rm6c9a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6zf7v4qz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zf7v4qz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_uj4upt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_uj4upt4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp92acq7l9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92acq7l9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9pishjzx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9pishjzx/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwg9_09sj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwg9_09sj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpst4apbl9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpst4apbl9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmplh7rkixt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplh7rkixt/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpjh90zdsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh90zdsv/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _________________________ test_nearest[None-True-same] _________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = True, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=True, E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd0nazken/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0nazken/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpflhjt_5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpflhjt_5w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnt3iy6gq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnt3iy6gq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp55qz6jtd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55qz6jtd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyrugco1x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrugco1x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 577246 587036 - 0 1 chr1 2447319 2447691 + 0 2 chr1 3005378 3014804 + 0 3 chr1 8532337 8537711 + 0 4 chr1 9952021 9958497 + 0 5 chrM 9380444 9383898 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9952021 | 9958497 | a | 0 | ... | | chr1 | 2447319 | 2447691 | a | 0 | ... | | chr1 | 3005378 | 3014804 | a | 0 | ... | | chr1 | 8532337 | 8537711 | a | 0 | ... | | chr1 | 577246 | 587036 | a | 0 | ... | | chrM | 9380444 | 9383898 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 6 rows and 12 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr1 577246 587036 - 0 1 chr1 2447319 2447691 + 0 2 chr1 3005378 3014804 + 0 3 chr1 8532337 8537711 + 0 5 chrM 9380444 9383898 + 0 0 chr1 9952021 9958497 + 0 df2 Chromosome Start End Strand Distance 0 chr1 577246 587036 - 0 1 chr1 2447319 2447691 + 0 2 chr1 3005378 3014804 + 0 3 chr1 8532337 8537711 + 0 5 chrM 9380444 9383898 + 0 4 chr1 9952021 9958497 + 0 Actual Chromosome Start End Strand Distance 0 chr1 577246 587036 - 0 1 chr1 2447319 2447691 + 0 2 chr1 3005378 3014804 + 0 3 chr1 8532337 8537711 + 0 4 chr1 9952021 9958497 + 0 5 chrM 9380444 9383898 + 0 Expected Chromosome Start End Strand Distance 0 chr1 577246 587036 - 0 1 chr1 2447319 2447691 + 0 2 chr1 3005378 3014804 + 0 3 chr1 8532337 8537711 + 0 4 chr1 9952021 9958497 + 0 5 chrM 9380444 9383898 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=6, step=1) Expected index RangeIndex(start=0, stop=6, step=1) index equal [ True True True True True True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1anyzffj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1anyzffj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpar2m90ei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpar2m90ei/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6k98fm7a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6k98fm7a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4djuwmm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4djuwmm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyc8wud7z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyc8wud7z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3idtldp8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3idtldp8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcuwh40w_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcuwh40w_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9je0827y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9je0827y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjt0q2kxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjt0q2kxc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr83k98_q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr83k98_q/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprx3_lqdo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprx3_lqdo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx368cetk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx368cetk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvmafo9hx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmafo9hx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf86voqyj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf86voqyj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdkzd32n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdkzd32n0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8y2gct6a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8y2gct6a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjjf9_doo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjf9_doo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxv0ayezu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxv0ayezu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp23rtykfz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp23rtykfz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1de8l0at/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1de8l0at/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplm8t3mi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplm8t3mi0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7qj8cpg4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7qj8cpg4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvzbu4e1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvzbu4e1s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5m62458q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5m62458q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphysvqma1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphysvqma1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc0q48mdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc0q48mdb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ____________________ test_k_nearest[None-False-False-last] _____________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = False, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=False, E strandedness=False, E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpeuzc_e5i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeuzc_e5i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcxm_kjel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxm_kjel/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_6ssoi_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_6ssoi_f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgdbbiy8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdbbiy8n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5krnu4l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5krnu4l8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpusgqs92j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpusgqs92j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxx4u_tom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxx4u_tom/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpcnpyqzte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcnpyqzte/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4jxphlm7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4jxphlm7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvwb4qqd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvwb4qqd3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpch_t18o8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpch_t18o8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw3xw3aw2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw3xw3aw2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc_w5wwn3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_w5wwn3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp33h1zl_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33h1zl_z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfx4bf1b3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfx4bf1b3/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgc_3p15f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgc_3p15f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpt2hlcf6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2hlcf6_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmprtrefa8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtrefa8k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9u6cfsfm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9u6cfsfm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7klh101k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7klh101k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpge1kbrdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpge1kbrdq/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfqqzx8r4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfqqzx8r4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp67i2toaf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp67i2toaf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw39fcn2t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw39fcn2t/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmp18d0a1ek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18d0a1ek/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -io -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdee14y24/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdee14y24/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr18 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr17 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. _______________________ test_nearest[None-True-opposite] _______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = True, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 73218 | 74756 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=True, E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RjLJzIwMDIkMkox8jAwAbEjAXe7ftAQnDACABUlAOf') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcvojzo02/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvojzo02/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqp0f2hqj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqp0f2hqj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7npyyfx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7npyyfx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnwrj3fwz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnwrj3fwz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpid03wxsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpid03wxsw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpywitvcph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpywitvcph/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkrwt_dl1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrwt_dl1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprormukve/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprormukve/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpux6cikdk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpux6cikdk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsz6vdkyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsz6vdkyu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptv0et510/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptv0et510/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4d08tf1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4d08tf1t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv8uod_nz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv8uod_nz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcvedi1a9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvedi1a9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1eilc0pn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1eilc0pn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp11m7j0ff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp11m7j0ff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcqriddkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcqriddkm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ubqrrip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ubqrrip/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeu5b630h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeu5b630h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpibv0q6wa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpibv0q6wa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpat8qszut/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpat8qszut/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp40vn6kol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40vn6kol/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl9nudksl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl9nudksl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd3dp3wj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3dp3wj8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0zaqkwzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0zaqkwzq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph_jmefql/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph_jmefql/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpscj_p_ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpscj_p_ky/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp83ye69dd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83ye69dd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4gysre4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4gysre4v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphd3d26h1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphd3d26h1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mhga7sb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mhga7sb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph4pumcc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph4pumcc6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3gj26u1l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gj26u1l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcsba13up/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcsba13up/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp65jdf45w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65jdf45w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg66n4abn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg66n4abn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm7jzwk58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm7jzwk58/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain84-method_chain84] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ___________________ test_k_nearest[None-True-opposite-last] ____________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = True, strandedness = 'opposite', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=True, E strandedness='opposite', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplp6nl6s7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplp6nl6s7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnbrnezl6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnbrnezl6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdigzlmzi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdigzlmzi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp79aphf_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79aphf_3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp91hfpl7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp91hfpl7i/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpputg9mmt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpputg9mmt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_k4xezlz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_k4xezlz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp3uj1aw_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3uj1aw_3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdf53c_2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf53c_2n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2hxhlth/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2hxhlth/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0fwqowz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fwqowz2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpk214jteb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk214jteb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmu24kbjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmu24kbjd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7defccyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7defccyg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpla4fuxlm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpla4fuxlm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpord56qr5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpord56qr5/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp62t8vqq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp62t8vqq2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8ru_i2r_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ru_i2r_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdrqqhh0c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdrqqhh0c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp20i12rz1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20i12rz1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpldlphwyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpldlphwyp/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphysomi4p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphysomi4p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyee1ara1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyee1ara1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp51zply7i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51zply7i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfite1suz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfite1suz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplm3y7are/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplm3y7are/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpw22vjrlk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw22vjrlk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpir4xbtua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpir4xbtua/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp1og06rdr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1og06rdr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgb76onad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgb76onad/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpikv_tdxv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpikv_tdxv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpm8nv4ssi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8nv4ssi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfyq47hj7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfyq47hj7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpliizliaw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpliizliaw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpyv_3x5js/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyv_3x5js/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuo7sl6wh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuo7sl6wh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfv9t3xgf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfv9t3xgf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgn27wb2y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgn27wb2y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpdcd0rwax/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcd0rwax/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp38k01lx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38k01lx9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8jyp3e8e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8jyp3e8e/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpa1ojux9j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1ojux9j/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp10uikvkf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp10uikvkf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpaqlwoej0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaqlwoej0/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphh55yv69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphh55yv69/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8pm9cf5c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pm9cf5c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpz814_dip/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz814_dip/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp0snz6d9c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0snz6d9c/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe0so5ul1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0so5ul1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzyw2vdgc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzyw2vdgc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmphwl3ri3i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwl3ri3i/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi539o06q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi539o06q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpht05b7f2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpht05b7f2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsijneeu7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsijneeu7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp39ig6lj_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp39ig6lj_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsnutezmk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsnutezmk/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplfou0u6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplfou0u6y/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc204pg4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc204pg4z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7s2k5_ab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s2k5_ab/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbg64hz36/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbg64hz36/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpiwqsqxho/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwqsqxho/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpgdf7gfmz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgdf7gfmz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpf71hc_yl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf71hc_yl/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmplh6cvpfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplh6cvpfi/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpi0a7q3tb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi0a7q3tb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppyykxj1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppyykxj1n/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmppqcl6vys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppqcl6vys/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmpbkzgms2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbkzgms2m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4mjf69sb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4mjf69sb/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -S -t last -a <(sort -k1,1 -k2,2n /tmp/tmptfma19o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfma19o0/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ________________________ test_nearest[None-False-False] ________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = False, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=False, E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiwoax6ew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiwoax6ew/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06gami35/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06gami35/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv4ceo62v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv4ceo62v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprn6k6ztp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprn6k6ztp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7e74_k71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7e74_k71/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiqfl0td1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiqfl0td1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp790k5ye1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp790k5ye1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpopnh3tqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpopnh3tqp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf8em3lr0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8em3lr0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwqvgxthy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqvgxthy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt2u5qv9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2u5qv9l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnt5i45dd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnt5i45dd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyn6p2x5d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyn6p2x5d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiq8htc8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiq8htc8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcuag9aok/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcuag9aok/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1orhjugr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1orhjugr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8svi5mnh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8svi5mnh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq2v4qia_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2v4qia_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp74ji17sh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp74ji17sh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5r1vsi4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5r1vsi4z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2hm5ltsb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2hm5ltsb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9x4s7uf9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9x4s7uf9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_rqm5a9u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_rqm5a9u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ef9i0b4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ef9i0b4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpydix2q9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpydix2q9t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyrlx7wm5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyrlx7wm5/f2.bed) ___________ test_three_in_a_row[strandedness_chain85-method_chain85] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain129-method_chain129] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 67334 | 67595 | a | 0 | + | E | chr1 | 524546 | 526596 | a | 0 | + | E | chr1 | 263682 | 263943 | a | 0 | + | E | chr14 | 263682 | 263943 | a | 0 | + | E | chr16 | 65545 | 65806 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66097 | 66358 | a | 0 | + | E | chr1 | 196869 | 198919 | a | 0 | + | E | chr1 | 263682 | 263943 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6967556 | 6968070 | a | 0 | - | E | chr1 | 8061954 | 8064859 | a | 0 | - | E | chr2 | 66245 | 69150 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicXY0/CsJQDIfzJe/5KiId6tbNQRE6uDt6AkGwuHQQQQQ3NxcP4+4lBA/hRRxNrZNZQn5/vlDNxu/EoX8zmvXryW5/3zBdXhtBZUgUCJLTAwRprwLJkIIUXbWsNUYkd8M35F7uFaFanE/8kKlDel0MnXvOPPPfIDqnRAO+rXvno86mPq4MiegDnVxCK23dKAe18AHlEhMC') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr2 | 67334 | 76239 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_k_nearest[None-True-same-last] ______________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = True, strandedness = 'same', ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=True, E strandedness='same', E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfikh4pr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfikh4pr2/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnmh4clbj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnmh4clbj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpabfqyymg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpabfqyymg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp6_m7bvsm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6_m7bvsm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4c7d5bjh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4c7d5bjh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpif_xs5r8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpif_xs5r8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpp2ne4xnn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp2ne4xnn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxwc6pym7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwc6pym7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmph1ktt76f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1ktt76f/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7dj3grha/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7dj3grha/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphimut5r8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphimut5r8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx4dxmgva/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx4dxmgva/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphplmxi1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphplmxi1s/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmphwvf75x1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphwvf75x1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpnvj8ot64/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnvj8ot64/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8rhumv6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8rhumv6b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpews0hrgo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpews0hrgo/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4qp39h7k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4qp39h7k/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpxlk5zhjj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxlk5zhjj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpfs3l82yh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfs3l82yh/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpx852gv42/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx852gv42/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpmvu4i76q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmvu4i76q/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuzsl6thz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuzsl6thz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc5a68z9m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5a68z9m/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp5dm7p4k7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5dm7p4k7/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -s -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4c1s3_0p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4c1s3_0p/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr2 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ________________________ test_nearest[None-False-same] _________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = False, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=False, E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8_i2b7vl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_i2b7vl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8pof51dk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pof51dk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchtfly9l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchtfly9l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppynxfsii/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppynxfsii/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8p_7p4q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8p_7p4q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq2z1ar_3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2z1ar_3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1ei7uhl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1ei7uhl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprs_yzan_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprs_yzan_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp31az1h5w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31az1h5w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf8kcbkgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf8kcbkgu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuozk1jzn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuozk1jzn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdvrimy2c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdvrimy2c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8nd0ph2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8nd0ph2z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppgm9chtp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppgm9chtp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpglqpnc3u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpglqpnc3u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe5xs07zc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe5xs07zc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpip83nodt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpip83nodt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7kfgcft0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7kfgcft0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpun9nja2z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpun9nja2z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwxtu_5jc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwxtu_5jc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprtu33ru4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtu33ru4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsiof1pq1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsiof1pq1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppm87is52/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppm87is52/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp90tbxxy3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp90tbxxy3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0e635c2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0e635c2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmv9v1dwl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmv9v1dwl/f2.bed) _____________________ test_k_nearest[None-True-False-last] _____________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = True, strandedness = False, ties = 'last' @pytest.mark.bedtools > @pytest.mark.explore tests/test_binary.py:510: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:548: in test_k_nearest result = gr.k_nearest( pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=True, E strandedness=False, E ties='last', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:29: ValueError ----------------------------- Captured stdout call ----------------------------- ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_1kvbyt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_1kvbyt4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpvysz__34/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvysz__34/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmps9kwb97z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9kwb97z/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp_2lhqhyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_2lhqhyn/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpj9dveggj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj9dveggj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpy3aqpxla/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy3aqpxla/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmptj4kztf_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj4kztf_/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmplgqkcqli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplgqkcqli/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpus8zti3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpus8zti3b/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp2141qe1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2141qe1d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp4zceu2b8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zceu2b8/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp9yelzuqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yelzuqm/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpo182qa4w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo182qa4w/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp60nxw9ab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp60nxw9ab/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmphlzir1kc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlzir1kc/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpuftsnmt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuftsnmt9/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp8182300d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8182300d/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpisieo1m1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisieo1m1/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpwvl9qngz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwvl9qngz/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpsfx63apj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfx63apj/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7wen7jt4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7wen7jt4/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpc1mctx5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc1mctx5l/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpzrj6ntau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzrj6ntau/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpkyjma3gf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyjma3gf/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmp7eyeku6a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7eyeku6a/f2.bed) ---------------------------------------------------------------------------------------------------- cmd cmd cmd cmd cmd bedtools closest -k 2 -D a -t last -a <(sort -k1,1 -k2,2n /tmp/tmpe24bl161/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe24bl161/f2.bed) ----------------------------- Captured stderr call ----------------------------- Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr12 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr19 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr21 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr22 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr5 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr7 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chrX than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr20 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr6 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. Warning: Fewer hits (1) found on chr1 than requested (2). It is likely that there are fewer total records on that chromosome than requested. ___________ test_three_in_a_row[strandedness_chain86-method_chain86] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') _________________________ test_k_nearest_1_vs_nearest __________________________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 @settings( > max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_binary.py:576: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:583: in test_k_nearest_1_vs_nearest result_k = gr.k_nearest(gr2, k=1, strandedness=None, overlap=True, how=None) pyranges/pyranges.py:2450: in k_nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/k_nearest.py:180: in _nearest df = __nearest(d1, d2, **kwargs) pyranges/methods/k_nearest.py:71: in nearest plidx, pridx, pdist = nearest_previous_idx(d1, d2, d1.__k__.values, ties) pyranges/methods/k_nearest.py:28: in nearest_previous_idx lidx, ridx_pos, dist = k_nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_k_nearest_1_vs_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/k_nearest.pyx:25: ValueError ____________ test_three_in_a_row[strandedness_chain0-method_chain0] ____________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ______________________ test_nearest[None-False-opposite] _______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = None, overlap = False, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how=None, E overlap=False, E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj2zywalg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj2zywalg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfe7et3gc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfe7et3gc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa44ijben/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa44ijben/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm9_qn8d5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9_qn8d5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpas1zpuyf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpas1zpuyf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3c53fj3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3c53fj3t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6o68ees5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6o68ees5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfis6vuyv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfis6vuyv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzv4gaxu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzv4gaxu2/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv3tn5pcy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv3tn5pcy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9sadk8yv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9sadk8yv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmperkrq282/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmperkrq282/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp38vho2ar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp38vho2ar/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn6h2j6dd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6h2j6dd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0ydvkj8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0ydvkj8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cuo2iin/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cuo2iin/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpodmh7j62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpodmh7j62/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6rsz8qtt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6rsz8qtt/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpww8bzlvp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpww8bzlvp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplys5hmhl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplys5hmhl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx58vrrqd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx58vrrqd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptzxtr654/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptzxtr654/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9_99mtra/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9_99mtra/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzb8_50cx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzb8_50cx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwqzmmix4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqzmmix4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp37y5gvtb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp37y5gvtb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprka76lli/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprka76lli/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyoexg0_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyoexg0_6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmox26q4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmox26q4v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppocztgyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppocztgyp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg97ospyv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg97ospyv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxwzzb8oi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwzzb8oi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmputqw_pte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmputqw_pte/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmply410d91/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmply410d91/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdta57i5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdta57i5p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfknl4br2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfknl4br2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp780vnr_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp780vnr_8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpvalj8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpvalj8g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77gx5wk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77gx5wk9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqhkiwuci/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqhkiwuci/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpki7nax_5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpki7nax_5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgbeoygt0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbeoygt0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjqw1k8ew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqw1k8ew/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp18hv8z71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp18hv8z71/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ffjw56l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ffjw56l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpksf30q6_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksf30q6_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfejpr1eb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfejpr1eb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptvlpswox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptvlpswox/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptx61j_71/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptx61j_71/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz5m5tlqs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz5m5tlqs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp__v_kmo0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp__v_kmo0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1rz5wgo5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1rz5wgo5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp22ckbibl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp22ckbibl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8wm_xs85/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8wm_xs85/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl1ufii7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl1ufii7l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg3bie5ld/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3bie5ld/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_dw3wmjr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_dw3wmjr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoloen6z5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoloen6z5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpivea7npr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivea7npr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcxu0e4_6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxu0e4_6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl2y0ivgo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl2y0ivgo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx947cmwj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx947cmwj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5uwobpeb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5uwobpeb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdcdtmbkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdcdtmbkk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7yd5sohv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7yd5sohv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy53cuyyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy53cuyyp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdojfimat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdojfimat/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgbn2dotj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbn2dotj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps30ckuy4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps30ckuy4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3avzeic5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3avzeic5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr7fl5_y0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr7fl5_y0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjgzusv1i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjgzusv1i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk3pmjdjo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk3pmjdjo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkrklde36/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkrklde36/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ob2ar9k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ob2ar9k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8mqzievh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8mqzievh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpku693_n8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpku693_n8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbikjnmew/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbikjnmew/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcmhr5h7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcmhr5h7q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5orosd76/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5orosd76/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsgy5xbt1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgy5xbt1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkg5m89_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkg5m89_z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5hyybm58/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hyybm58/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk2d9h_mb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2d9h_mb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp26tlzr_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp26tlzr_h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpogarfg66/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpogarfg66/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp55u3fzm3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp55u3fzm3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5xw9gezf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5xw9gezf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpafgc46ph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpafgc46ph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb72sjpl3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb72sjpl3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd0pg0kbn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd0pg0kbn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkkuypwq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkkuypwq5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa1sfq3ms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1sfq3ms/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu5lgsjjr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5lgsjjr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa1g4a827/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa1g4a827/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjuvs6an6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjuvs6an6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2n7apz61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2n7apz61/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd66mcfn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd66mcfn_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpay232ih1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpay232ih1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi446hrs4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi446hrs4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpitxpbdfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpitxpbdfh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphox69_pf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphox69_pf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzx8_072b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzx8_072b/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppz9p5ofa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppz9p5ofa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm9r_l9cf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9r_l9cf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuz2mtma5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuz2mtma5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmo_1_auh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo_1_auh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8p6l1k1n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8p6l1k1n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph5w1a0w9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5w1a0w9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3vgnie3h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vgnie3h/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu3fp9eer/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu3fp9eer/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptqwjowwd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqwjowwd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvtf071jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtf071jk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeoxh6mzw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeoxh6mzw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6e6ujd77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6e6ujd77/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpliklle5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpliklle5e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp46qu94wg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp46qu94wg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4zz1p4m8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zz1p4m8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsph_qxwx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsph_qxwx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplbe5is6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplbe5is6b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk2i8cs21/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk2i8cs21/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6x5v082l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6x5v082l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpau39d0k6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpau39d0k6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp09bl3x7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp09bl3x7_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpejbb_trr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejbb_trr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_8ohrg14/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_8ohrg14/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcbbpuzf7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcbbpuzf7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt4men5rn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt4men5rn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp117537l9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp117537l9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplto805xj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplto805xj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx3qlpwg6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx3qlpwg6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr13_ezse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr13_ezse/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn54p2g1s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn54p2g1s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvm1gwfbw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvm1gwfbw/f2.bed) __________ test_three_in_a_row[strandedness_chain131-method_chain131] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ___________ test_three_in_a_row[strandedness_chain87-method_chain87] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ____________ test_three_in_a_row[strandedness_chain1-method_chain1] ____________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', False), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain158-method_chain158] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain159-method_chain159] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ___________ test_three_in_a_row[strandedness_chain88-method_chain88] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain133-method_chain133] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ______________________ test_nearest[upstream-True-False] _______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = True, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=True, E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyovvw14z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyovvw14z/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3yt9ytyp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3yt9ytyp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps085zm4h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps085zm4h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7hjey2o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7hjey2o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3kith4wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kith4wv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyj2nvkx8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyj2nvkx8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm8b0leqm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm8b0leqm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6847099 6848078 + 0 1 chr1 7896375 7897839 + 0 2 chr16 5647521 5657494 + 0 3 chr19 837391 845095 - 0 4 chr21 2263563 2263564 - 0 5 chr21 4873549 4883361 - 0 6 chr21 7873939 7873940 - 0 7 chr22 914323 914325 + 0 8 chrX 927291 930050 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6847099 | 6848078 | a | 0 | ... | | chr1 | 7896375 | 7897839 | a | 0 | ... | | chr16 | 5647521 | 5657494 | a | 0 | ... | | chr19 | 837391 | 845095 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr21 | 7873939 | 7873940 | a | 0 | ... | | chr21 | 4873549 | 4883361 | a | 0 | ... | | chr21 | 2263563 | 2263564 | a | 0 | ... | | chr22 | 914323 | 914325 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr19 837391 845095 - 0 7 chr22 914323 914325 + 0 8 chrX 927291 930050 - 0 6 chr21 2263563 2263564 - 0 5 chr21 4873549 4883361 - 0 2 chr16 5647521 5657494 + 0 0 chr1 6847099 6848078 + 0 4 chr21 7873939 7873940 - 0 1 chr1 7896375 7897839 + 0 df2 Chromosome Start End Strand Distance 3 chr19 837391 845095 - 0 7 chr22 914323 914325 + 0 8 chrX 927291 930050 - 0 4 chr21 2263563 2263564 - 0 5 chr21 4873549 4883361 - 0 2 chr16 5647521 5657494 + 0 0 chr1 6847099 6848078 + 0 6 chr21 7873939 7873940 - 0 1 chr1 7896375 7897839 + 0 Actual Chromosome Start End Strand Distance 0 chr1 6847099 6848078 + 0 1 chr1 7896375 7897839 + 0 2 chr16 5647521 5657494 + 0 3 chr19 837391 845095 - 0 4 chr21 2263563 2263564 - 0 5 chr21 4873549 4883361 - 0 6 chr21 7873939 7873940 - 0 7 chr22 914323 914325 + 0 8 chrX 927291 930050 - 0 Expected Chromosome Start End Strand Distance 0 chr1 6847099 6848078 + 0 1 chr1 7896375 7897839 + 0 2 chr16 5647521 5657494 + 0 3 chr19 837391 845095 - 0 4 chr21 2263563 2263564 - 0 5 chr21 4873549 4883361 - 0 6 chr21 7873939 7873940 - 0 7 chr22 914323 914325 + 0 8 chrX 927291 930050 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdczumdct/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdczumdct/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpisphu71g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpisphu71g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphlhu098s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphlhu098s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpks63347i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpks63347i/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx9nn3pir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx9nn3pir/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8d33o_zr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8d33o_zr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpup6whbei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpup6whbei/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjdubr1gm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdubr1gm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwsnrh_jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsnrh_jl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpipujm4wl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpipujm4wl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa2u809m6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa2u809m6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu7ambojk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu7ambojk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkk3d5kf0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkk3d5kf0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf4qxj2e7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf4qxj2e7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn_3gocom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn_3gocom/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoma28tkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoma28tkw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2pwolgtb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2pwolgtb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxt450vnv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxt450vnv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu2wagauo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu2wagauo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw01vqko1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw01vqko1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpunfe8_lj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpunfe8_lj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnn13w8il/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnn13w8il/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprzv0d3av/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzv0d3av/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp72zwe9ix/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp72zwe9ix/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujgzpzy8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujgzpzy8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpurq7za06/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpurq7za06/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp65og7eek/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp65og7eek/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp15ebmgcl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15ebmgcl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw95yq3qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw95yq3qx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnp2chklt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnp2chklt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzm9qybu5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzm9qybu5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1gvom7v2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1gvom7v2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu947wk2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu947wk2m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnjfm98yy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnjfm98yy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6uecyouo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6uecyouo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpygjc6tzz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpygjc6tzz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbcr88xj9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbcr88xj9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb45cwq6a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb45cwq6a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp_xc4q2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_xc4q2d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaecl7fiz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaecl7fiz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwgpx5npj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwgpx5npj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu9b8tw_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu9b8tw_9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwuzmy390/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwuzmy390/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxrsxaqeh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxrsxaqeh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6wzvzpq4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6wzvzpq4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuqy8ydd7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuqy8ydd7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu5n0qo6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5n0qo6o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8a4dsepa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8a4dsepa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp93petchj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp93petchj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv9lm6aeg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9lm6aeg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpffb_020m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpffb_020m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoxhx103v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoxhx103v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc7qoto6b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc7qoto6b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchp9jadr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchp9jadr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_vc6m4v6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_vc6m4v6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpebr9ca_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpebr9ca_7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0fl8waw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0fl8waw1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptw5821xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptw5821xp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2i17hngo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2i17hngo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4x3e8oz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4x3e8oz_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpseg2_mas/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpseg2_mas/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9v3v4tk9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9v3v4tk9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptwqwsaar/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptwqwsaar/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpohpk_knt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohpk_knt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv5evouam/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv5evouam/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq9hf03rw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq9hf03rw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3lv92zgn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3lv92zgn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8iykbfep/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8iykbfep/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkywuh44v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkywuh44v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mpz83sg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mpz83sg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp98qgniue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp98qgniue/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 257 262 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 262 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 257 262 + 0 df2 Chromosome Start End Strand Distance 0 chr1 257 262 + 0 Actual Chromosome Start End Strand Distance 0 chr1 257 262 + 0 Expected Chromosome Start End Strand Distance 0 chr1 257 262 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphjlc_9m9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphjlc_9m9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps0v681qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0v681qx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo35m00un/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo35m00un/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu_2hputq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_2hputq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprysp3o7e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprysp3o7e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj388yvfa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj388yvfa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain160-method_chain160] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain134-method_chain134] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ___________ test_three_in_a_row[strandedness_chain89-method_chain89] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain161-method_chain161] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain135-method_chain135] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') _______________________ test_nearest[upstream-True-same] _______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = True, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=True, E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfibmrunv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfibmrunv/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdwh51vns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwh51vns/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpprqnvudz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpprqnvudz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 6775 + 0 1 chr1 262474 267853 - 0 2 chr1 5129429 5134808 - 0 3 chr1 5176468 5181847 - 0 4 chr1 8186129 8186945 - 0 5 chr1 8329454 8334833 + 0 6 chr15 8329454 8332419 + 0 7 chr2 4886460 4891839 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 6775 | a | 0 | ... | | chr1 | 8329454 | 8334833 | a | 0 | ... | | chr1 | 5176468 | 5181847 | a | 0 | ... | | chr1 | 262474 | 267853 | a | 0 | ... | | chr1 | 5129429 | 5134808 | a | 0 | ... | | chr1 | 8186129 | 8186945 | a | 0 | ... | | chr2 | 4886460 | 4891839 | a | 0 | ... | | chr15 | 8329454 | 8332419 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 8 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 6775 + 0 3 chr1 262474 267853 - 0 6 chr2 4886460 4891839 + 0 4 chr1 5129429 5134808 - 0 2 chr1 5176468 5181847 - 0 5 chr1 8186129 8186945 - 0 7 chr15 8329454 8332419 + 0 1 chr1 8329454 8334833 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 6775 + 0 1 chr1 262474 267853 - 0 7 chr2 4886460 4891839 + 0 2 chr1 5129429 5134808 - 0 3 chr1 5176468 5181847 - 0 4 chr1 8186129 8186945 - 0 6 chr15 8329454 8332419 + 0 5 chr1 8329454 8334833 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 6775 + 0 1 chr1 262474 267853 - 0 2 chr1 5129429 5134808 - 0 3 chr1 5176468 5181847 - 0 4 chr1 8186129 8186945 - 0 5 chr1 8329454 8334833 + 0 6 chr15 8329454 8332419 + 0 7 chr2 4886460 4891839 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 6775 + 0 1 chr1 262474 267853 - 0 2 chr1 5129429 5134808 - 0 3 chr1 5176468 5181847 - 0 4 chr1 8186129 8186945 - 0 5 chr1 8329454 8334833 + 0 6 chr15 8329454 8332419 + 0 7 chr2 4886460 4891839 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=8, step=1) Expected index RangeIndex(start=0, stop=8, step=1) index equal [ True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo4bqv7my/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo4bqv7my/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdq3nw8jz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdq3nw8jz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpubgnp7rp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpubgnp7rp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6zcj1vl3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6zcj1vl3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpksprg25v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksprg25v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7053864 7063864 - 0 1 chr1 8170626 8180626 + 0 2 chr10 1636036 1646036 - 0 3 chr11 7115591 7118839 + 0 4 chr15 772274 782274 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8170626 | 8180626 | a | 0 | ... | | chr1 | 7053864 | 7063864 | a | 0 | ... | | chr10 | 1636036 | 1646036 | a | 0 | ... | | chr11 | 7115591 | 7118839 | a | 0 | ... | | chr15 | 772274 | 782274 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr15 772274 782274 + 0 2 chr10 1636036 1646036 - 0 1 chr1 7053864 7063864 - 0 3 chr11 7115591 7118839 + 0 0 chr1 8170626 8180626 + 0 df2 Chromosome Start End Strand Distance 4 chr15 772274 782274 + 0 2 chr10 1636036 1646036 - 0 0 chr1 7053864 7063864 - 0 3 chr11 7115591 7118839 + 0 1 chr1 8170626 8180626 + 0 Actual Chromosome Start End Strand Distance 0 chr1 7053864 7063864 - 0 1 chr1 8170626 8180626 + 0 2 chr10 1636036 1646036 - 0 3 chr11 7115591 7118839 + 0 4 chr15 772274 782274 + 0 Expected Chromosome Start End Strand Distance 0 chr1 7053864 7063864 - 0 1 chr1 8170626 8180626 + 0 2 chr10 1636036 1646036 - 0 3 chr11 7115591 7118839 + 0 4 chr15 772274 782274 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpohhxkv62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpohhxkv62/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe_woif3y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe_woif3y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 7053864 7063864 - 0 1 chr1 8170626 8180626 + 0 2 chr10 1636036 1646036 - 0 3 chr11 7115591 7118839 + 0 4 chr15 772274 782274 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8170626 | 8180626 | a | 0 | ... | | chr1 | 7053864 | 7063864 | a | 0 | ... | | chr10 | 1636036 | 1646036 | a | 0 | ... | | chr11 | 7115591 | 7118839 | a | 0 | ... | | chr15 | 772274 | 782274 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 4 chr15 772274 782274 + 0 2 chr10 1636036 1646036 - 0 1 chr1 7053864 7063864 - 0 3 chr11 7115591 7118839 + 0 0 chr1 8170626 8180626 + 0 df2 Chromosome Start End Strand Distance 4 chr15 772274 782274 + 0 2 chr10 1636036 1646036 - 0 0 chr1 7053864 7063864 - 0 3 chr11 7115591 7118839 + 0 1 chr1 8170626 8180626 + 0 Actual Chromosome Start End Strand Distance 0 chr1 7053864 7063864 - 0 1 chr1 8170626 8180626 + 0 2 chr10 1636036 1646036 - 0 3 chr11 7115591 7118839 + 0 4 chr15 772274 782274 + 0 Expected Chromosome Start End Strand Distance 0 chr1 7053864 7063864 - 0 1 chr1 8170626 8180626 + 0 2 chr10 1636036 1646036 - 0 3 chr11 7115591 7118839 + 0 4 chr15 772274 782274 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaa1a4e22/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaa1a4e22/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5u4e_1x0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5u4e_1x0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfpiv31j9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfpiv31j9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplud8hwwi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplud8hwwi/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsklohgre/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsklohgre/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi8encqkw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8encqkw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ilyt1u6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ilyt1u6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpthi7z8or/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpthi7z8or/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcvzgoypc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcvzgoypc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpik5i746u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpik5i746u/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwzlveupj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwzlveupj/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzpmq4ujz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpmq4ujz/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp4sxmfty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp4sxmfty/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw5ohwsh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw5ohwsh5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3azx8456/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3azx8456/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1uw280ua/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1uw280ua/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpegydtn5k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpegydtn5k/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprtajgzjg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprtajgzjg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbqd3hxnz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbqd3hxnz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpukvmrdpx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpukvmrdpx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpudne7vww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpudne7vww/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp40gmpfr2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40gmpfr2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb75cra62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb75cra62/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7uqyrad/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7uqyrad/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplcj46_un/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcj46_un/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5d_40a8h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5d_40a8h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa3sga1z7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa3sga1z7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2jyg9lq5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2jyg9lq5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjksumxkj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjksumxkj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmfkn0aak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmfkn0aak/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwfnd29jb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwfnd29jb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxgmdiksb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxgmdiksb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xgrda0x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xgrda0x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpepo2emwf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepo2emwf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbslxr33v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbslxr33v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5hsd4n17/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hsd4n17/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvvcvy0qr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvvcvy0qr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8lp00tc8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8lp00tc8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzpm_buy6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzpm_buy6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkc0wln8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkc0wln8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj5cuq9zj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj5cuq9zj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpksympsf8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpksympsf8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzf_uw6zn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzf_uw6zn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz4psjhqf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz4psjhqf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmg8li_e7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmg8li_e7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdagmifgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdagmifgj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9y6jbe5v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9y6jbe5v/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgptm47fm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgptm47fm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmv9eof10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmv9eof10/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzjn4j9ue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzjn4j9ue/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqucm83xp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqucm83xp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1o9vk2l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1o9vk2l/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjc_teuud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjc_teuud/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoa4moyrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoa4moyrr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpivw0nkvd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpivw0nkvd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1lwcjcau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1lwcjcau/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7xo38kny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7xo38kny/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjvk1hezf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjvk1hezf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptl8pgtqn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptl8pgtqn/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsrmcdxn0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsrmcdxn0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_rol5jbd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_rol5jbd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw0p8u1x1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw0p8u1x1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_t9bibbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_t9bibbp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp67yre5a0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp67yre5a0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm6n60mnr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6n60mnr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpklrze9mi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklrze9mi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpve5qakhz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpve5qakhz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmqjx04_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqjx04_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwb5ooz7f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwb5ooz7f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4nimalh5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4nimalh5/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe33nfjau/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe33nfjau/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpenu4jgo4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpenu4jgo4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpduhbe2q3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpduhbe2q3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr76thha5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr76thha5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36le1tb0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36le1tb0/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv1bs1udx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv1bs1udx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmkx67d9x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmkx67d9x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplv3q89ur/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplv3q89ur/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpba4_0qio/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpba4_0qio/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain90-method_chain90] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'same'), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain162-method_chain162] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain136-method_chain136] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') _____________________ test_nearest[upstream-True-opposite] _____________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = True, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=True, E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvoeksz1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvoeksz1u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxx6i6cxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxx6i6cxr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkosetvga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkosetvga/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ylxl2ik/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ylxl2ik/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbv6dsajq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbv6dsajq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv86elrj9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv86elrj9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeqprd190/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeqprd190/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzs_1s8m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzs_1s8m/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_thmm9fg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_thmm9fg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr32u3as7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr32u3as7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf2b82__t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2b82__t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd6vu_o4y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6vu_o4y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp27ep8c7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp27ep8c7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpba06ohqc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpba06ohqc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkjc3zleh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkjc3zleh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5alycotl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5alycotl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphttjd7tt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphttjd7tt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbn1qfovj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbn1qfovj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1f7yx3jr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1f7yx3jr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxezpoxnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxezpoxnc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8f7xade4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8f7xade4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfn4raw90/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfn4raw90/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe6lbl2n7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe6lbl2n7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy17pwepl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy17pwepl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7igkfcno/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7igkfcno/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp17papuyr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp17papuyr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps3wlqxft/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3wlqxft/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xeov5tu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xeov5tu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxreb2jwy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxreb2jwy/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo0_fmzkk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo0_fmzkk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiuj5ymeb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiuj5ymeb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbx5d89p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbx5d89p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0rgyqk5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0rgyqk5p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplxmrhdyg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplxmrhdyg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzegxva6x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzegxva6x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpicoo29bq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpicoo29bq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqfpl_ln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqfpl_ln/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1pby7u5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1pby7u5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphudtbtg0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphudtbtg0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjz4vt2v2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjz4vt2v2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmcpawad3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmcpawad3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphw5eevq_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphw5eevq_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsydb9jma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsydb9jma/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxmpy1icy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxmpy1icy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeh2zvxui/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeh2zvxui/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5xp43o6o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5xp43o6o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkawn5ifl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkawn5ifl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsc_lcgnc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsc_lcgnc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6popzdnr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6popzdnr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3p9fwp2k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3p9fwp2k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptlc_u14c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptlc_u14c/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzhkva198/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzhkva198/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwyx12par/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyx12par/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4t4lpije/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4t4lpije/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvhywbcjw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvhywbcjw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf6_opyue/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf6_opyue/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc_thofv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_thofv_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx45wvmhy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx45wvmhy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpesku3590/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpesku3590/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9yn37uz3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9yn37uz3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmqv74fj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqv74fj3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe81tk3l8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe81tk3l8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpit1d5u7n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpit1d5u7n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmnr68p7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmnr68p7y/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpweozrq4j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpweozrq4j/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp43lo2ewh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp43lo2ewh/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6ksec1dz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6ksec1dz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0pfx79k6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0pfx79k6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkv1ofz7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkv1ofz7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxf9x83k8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxf9x83k8/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1282 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc6h8x1mf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc6h8x1mf/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd067rkrr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd067rkrr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl01jiyi0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl01jiyi0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6eqvvyn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6eqvvyn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy_b5m1sx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy_b5m1sx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph5u4wv59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph5u4wv59/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp89nfbda_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp89nfbda_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_awsbv8a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_awsbv8a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf5__rilf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf5__rilf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_74cvphe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_74cvphe/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp82o3qrqa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp82o3qrqa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp66xc2syb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp66xc2syb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1jiqii5l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1jiqii5l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn2r7gx9o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn2r7gx9o/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5mecd0_7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5mecd0_7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzs813vw9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzs813vw9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps322gsmr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps322gsmr/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1282 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2cq2r6pk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2cq2r6pk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuyei6vns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuyei6vns/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp45q5ekc6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp45q5ekc6/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcunvvzw9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcunvvzw9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzwx3hqz_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzwx3hqz_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp24cq5ka2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp24cq5ka2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsyvci731/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsyvci731/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpocpyl7jk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpocpyl7jk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -id -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiehr_swx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiehr_swx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain91-method_chain91] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain137-method_chain137] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[upstream-False-False] ______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = False, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:118: in _nearest r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=False, E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdtzbi6j2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdtzbi6j2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpum74jg9i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpum74jg9i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpizenlj_e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpizenlj_e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj8457o7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj8457o7t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz8j2goel/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8j2goel/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1u5ozmp3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1u5ozmp3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptpxc1i3q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpxc1i3q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfd4yhbgr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfd4yhbgr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq7f3n1p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq7f3n1p4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjqgoa5px/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjqgoa5px/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqi6dpqvh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqi6dpqvh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf9nbc7kc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf9nbc7kc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeasnlbbh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeasnlbbh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp895_8vxc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp895_8vxc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87gf2zsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87gf2zsu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2gy0jhru/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2gy0jhru/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprye_pkka/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprye_pkka/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvxfeq7yc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvxfeq7yc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyof9who7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyof9who7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd7b0onxr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7b0onxr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps3_qo0dt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps3_qo0dt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyf4nq7aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf4nq7aq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkfw07kp6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkfw07kp6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps67bj6qx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps67bj6qx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxg9vn8s0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxg9vn8s0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2ywd6jzq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2ywd6jzq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6bperr4j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6bperr4j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps1optt_h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps1optt_h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwidlrgsl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwidlrgsl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpse5lmsbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpse5lmsbm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk93z2zz2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk93z2zz2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5png9c8r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5png9c8r/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpql16j3oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpql16j3oo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7mmhiwfi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7mmhiwfi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpofzw8zub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpofzw8zub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsudx058q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsudx058q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp79xib1v3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp79xib1v3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdm_1yg92/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdm_1yg92/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8hhqqrji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8hhqqrji/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_cfdsild/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_cfdsild/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp92pbmx8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92pbmx8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl5ju79vl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl5ju79vl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprdgxynuk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprdgxynuk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkb0myyme/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkb0myyme/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpey4n35d3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpey4n35d3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp40wehy6e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp40wehy6e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_i0qzpkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_i0qzpkl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq74xwzzj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq74xwzzj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxw_5q15t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxw_5q15t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1kpo8df3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1kpo8df3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpto65mmpi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpto65mmpi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptmztmif5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptmztmif5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2j_98p3e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2j_98p3e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2_dbt_nt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2_dbt_nt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvmidxzjd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvmidxzjd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6iva3kpl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6iva3kpl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbo88509b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbo88509b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpye6i2n3j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpye6i2n3j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3rh8kf62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3rh8kf62/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ovx8pot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ovx8pot/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpqygi5e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpqygi5e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36r8fh8t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36r8fh8t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyzxtsqag/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyzxtsqag/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpadgyeoxa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadgyeoxa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0i676xuv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0i676xuv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa4xt84a7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4xt84a7/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain92-method_chain92] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain138-method_chain138] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ______________________ test_nearest[upstream-False-same] _______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = False, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:118: in _nearest r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=False, E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsgt_ow6u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgt_ow6u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp96rol6mh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp96rol6mh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6u2nost7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6u2nost7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp180811lo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp180811lo/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_7otxvf_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_7otxvf_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmhg9t_6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmhg9t_6h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc157n3tu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc157n3tu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjdoxx4j7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjdoxx4j7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_x7k7o26/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_x7k7o26/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9hj5ksid/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9hj5ksid/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpklf3fjx9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpklf3fjx9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1ib_szqi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1ib_szqi/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_d0abjs0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_d0abjs0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xfgba39/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xfgba39/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpepysvrlo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpepysvrlo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpox0ycvz9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpox0ycvz9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9tlkbzcg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tlkbzcg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77kowlph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77kowlph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12ay80vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12ay80vr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplaqlfgn5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplaqlfgn5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcb8vus_1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcb8vus_1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp719msk6g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp719msk6g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx72icg6w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx72icg6w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn6lyfoby/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn6lyfoby/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbk_ts4t4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbk_ts4t4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm9ccq011/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm9ccq011/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt1asnbbi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt1asnbbi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphw_0u96p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphw_0u96p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnyy0xvgh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnyy0xvgh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfrx94toa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfrx94toa/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxcmfii_x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxcmfii_x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt2l1gv84/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt2l1gv84/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpujt9v3it/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpujt9v3it/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5pgvhn_a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5pgvhn_a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppey3ztom/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppey3ztom/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph2atbfu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph2atbfu_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqa0319b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqa0319b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqmzj85jy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqmzj85jy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz70o7vop/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz70o7vop/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfema0ltf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfema0ltf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptyvatfl7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptyvatfl7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6vm83gaa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6vm83gaa/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzmcdlx2d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzmcdlx2d/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzy0_xr1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzy0_xr1d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyhvkfknw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyhvkfknw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfjvzzksi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfjvzzksi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv9yj8ncf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9yj8ncf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1e302r8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1e302r8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr3p_8fdb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr3p_8fdb/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain166-method_chain166] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 68867 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2AAAkYWRiBgYGRICT0N5AERELPwAAkAGUcBow==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain139-method_chain139] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ____________________ test_nearest[upstream-False-opposite] _____________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'upstream', overlap = False, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:118: in _nearest r_idx, dist = _previous_nonoverlapping(df_to_find_nearest_in.Start, pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='upstream', E overlap=False, E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpslnrk59o/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpslnrk59o/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7sm217gu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sm217gu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmgsqwwms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmgsqwwms/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5l6xnaye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5l6xnaye/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi8ksf2vu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8ksf2vu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg7ogx_q7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg7ogx_q7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp20w443kz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp20w443kz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm_ieawx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm_ieawx5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1fm8uzox/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fm8uzox/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpot78e0i6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpot78e0i6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyf0eu4eq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyf0eu4eq/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgrc0_yb_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgrc0_yb_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpomypm0xb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpomypm0xb/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfbhmmrsu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfbhmmrsu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppytcqk28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppytcqk28/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbxg7sua5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbxg7sua5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2quuz2bm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2quuz2bm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3m0k9ohe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3m0k9ohe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwuf37ndg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwuf37ndg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptz7d0rzu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptz7d0rzu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmqaudy0k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmqaudy0k/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprzh_wr48/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprzh_wr48/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0wiftdot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0wiftdot/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptp9yj_m9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptp9yj_m9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi_s8shxe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi_s8shxe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp883z2pei/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp883z2pei/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1q898ydu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1q898ydu/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2esx1j3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2esx1j3l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc85bl4tk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc85bl4tk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt0ufa7kk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0ufa7kk/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9t89o4wq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9t89o4wq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt8maw2oy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt8maw2oy/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgy_49ch1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgy_49ch1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsgy6i8v3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsgy6i8v3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt54hxwj4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt54hxwj4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps4jqey_f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps4jqey_f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnsmuz6b2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnsmuz6b2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpggkvn8lr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpggkvn8lr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ypstt_z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ypstt_z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmporjmh267/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmporjmh267/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2mqihyr3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2mqihyr3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps0lzrstj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps0lzrstj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp80w8cl01/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp80w8cl01/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgqjgn2az/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgqjgn2az/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppp76htbp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppp76htbp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1v37c7mf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1v37c7mf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpknnrilr7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpknnrilr7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpweal4bk6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpweal4bk6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl0ref8r2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl0ref8r2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdosf66k0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdosf66k0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwq_tqsb5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwq_tqsb5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptj2j_u53/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptj2j_u53/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwlj1tw5j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwlj1tw5j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9f6vx6er/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9f6vx6er/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_odrbn5x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_odrbn5x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1y0c6h7q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1y0c6h7q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyu6nuo8x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyu6nuo8x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3aqhjh0i/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3aqhjh0i/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3v78ag0f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3v78ag0f/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdzvl2ia1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdzvl2ia1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplpwbbgj2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplpwbbgj2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpns3fxdzd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpns3fxdzd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr0so_5s8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0so_5s8/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpchmjvnig/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpchmjvnig/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9ca5xic_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9ca5xic_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4lfzwpeg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4lfzwpeg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6801tume/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6801tume/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp28pw2i8n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28pw2i8n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp87mydda9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp87mydda9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc10ufabw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc10ufabw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfednbgff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfednbgff/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0mxcuw4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mxcuw4a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp33w3dxr7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp33w3dxr7/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxedvb0q4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxedvb0q4/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy72sp4_n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy72sp4_n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5vaqdpv5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vaqdpv5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpaq_nbjnn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpaq_nbjnn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpncoclbdg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncoclbdg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9zku88l6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9zku88l6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3kvir4dw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3kvir4dw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp99k1kl56/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp99k1kl56/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp31ddds8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp31ddds8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt6lgc2aq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt6lgc2aq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxmrdmg9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxmrdmg9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu50tdvrz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu50tdvrz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxw1ohanb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxw1ohanb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo8kqls3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo8kqls3x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5vipw8sl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5vipw8sl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpduhufgse/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpduhufgse/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsmufh5de/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsmufh5de/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyt8gkwg8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyt8gkwg8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf0dtt3de/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf0dtt3de/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoadesxzh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoadesxzh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu5h05k77/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu5h05k77/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe2xyzvjf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe2xyzvjf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqq09uw6d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqq09uw6d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptt9jklfs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptt9jklfs/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5q16ij_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5q16ij_d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwexfx0sj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwexfx0sj/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppkok6kpg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppkok6kpg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbtuw5s6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbtuw5s6p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptupnbyjx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptupnbyjx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmpvuzdz6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmpvuzdz6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfyb5axw1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfyb5axw1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphbjt58ff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphbjt58ff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpj_4zdenl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpj_4zdenl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_txf_tat/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_txf_tat/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgzcgclq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgzcgclq2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplp34pnbl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplp34pnbl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi5x3a0wo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5x3a0wo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxqkp8fwp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxqkp8fwp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp_a3f1m4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp_a3f1m4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp78kalb4k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp78kalb4k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpo1j3xqk8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpo1j3xqk8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprjtftmfg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprjtftmfg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0ppex797/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0ppex797/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0mpj73p4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0mpj73p4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkyh4aenb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkyh4aenb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpga6b9t5_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpga6b9t5_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmbr4idhn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbr4idhn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcf1a12w5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcf1a12w5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkwsdl9qd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkwsdl9qd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8u7eyu1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8u7eyu1u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd6nvjq63/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd6nvjq63/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1fsuv_sd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1fsuv_sd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp06ojv5qi/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp06ojv5qi/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiu8cejj1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiu8cejj1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpte70xtbu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpte70xtbu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3l40o0lm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3l40o0lm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpejfwvkrg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpejfwvkrg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp28u35rtv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp28u35rtv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgaxa_y6a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgaxa_y6a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3zw66cnf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3zw66cnf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1casrla1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1casrla1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps71nb_bf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps71nb_bf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -id -D a -S -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfsdo2v9t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfsdo2v9t/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain140-method_chain140] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ___________ test_three_in_a_row[strandedness_chain96-method_chain96] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'same'), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain168-method_chain168] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain141-method_chain141] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') _____________________ test_nearest[downstream-True-False] ______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = True, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=True, E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4wrev1ub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4wrev1ub/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqvojm59a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqvojm59a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpevo4ur3l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpevo4ur3l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq5g24oma/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq5g24oma/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3677836 3678204 + 0 1 chr1 3677836 3678204 - 0 2 chr1 3677836 3678204 - 0 3 chr1 3677836 3681710 + 0 4 chr1 3677836 3682160 - 0 5 chr13 3677836 3678204 + 0 6 chr21 3677836 3679966 - 0 7 chrM 3677836 3678204 - 0 8 chrY 3677836 3678204 - 0 9 chrY 3677836 3687836 - 0 10 chrY 8370657 8370712 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3677836 | 3678204 | a | 0 | ... | | chr1 | 3677836 | 3681710 | a | 0 | ... | | chr1 | 3677836 | 3678204 | a | 0 | ... | | chr1 | 3677836 | 3678204 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chrM | 3677836 | 3678204 | a | 0 | ... | | chrY | 3677836 | 3687836 | a | 0 | ... | | chrY | 3677836 | 3678204 | a | 0 | ... | | chrY | 8370657 | 8370712 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 3677836 3678204 + 0 2 chr1 3677836 3678204 - 0 3 chr1 3677836 3678204 - 0 5 chr13 3677836 3678204 + 0 7 chrM 3677836 3678204 - 0 9 chrY 3677836 3678204 - 0 6 chr21 3677836 3679966 - 0 1 chr1 3677836 3681710 + 0 4 chr1 3677836 3682160 - 0 8 chrY 3677836 3687836 - 0 10 chrY 8370657 8370712 - 0 df2 Chromosome Start End Strand Distance 0 chr1 3677836 3678204 + 0 1 chr1 3677836 3678204 - 0 2 chr1 3677836 3678204 - 0 5 chr13 3677836 3678204 + 0 7 chrM 3677836 3678204 - 0 8 chrY 3677836 3678204 - 0 6 chr21 3677836 3679966 - 0 3 chr1 3677836 3681710 + 0 4 chr1 3677836 3682160 - 0 9 chrY 3677836 3687836 - 0 10 chrY 8370657 8370712 - 0 Actual Chromosome Start End Strand Distance 0 chr1 3677836 3678204 + 0 1 chr1 3677836 3678204 - 0 2 chr1 3677836 3678204 - 0 3 chr1 3677836 3681710 + 0 4 chr1 3677836 3682160 - 0 5 chr13 3677836 3678204 + 0 6 chr21 3677836 3679966 - 0 7 chrM 3677836 3678204 - 0 8 chrY 3677836 3678204 - 0 9 chrY 3677836 3687836 - 0 10 chrY 8370657 8370712 - 0 Expected Chromosome Start End Strand Distance 0 chr1 3677836 3678204 + 0 1 chr1 3677836 3678204 - 0 2 chr1 3677836 3678204 - 0 3 chr1 3677836 3681710 + 0 4 chr1 3677836 3682160 - 0 5 chr13 3677836 3678204 + 0 6 chr21 3677836 3679966 - 0 7 chrM 3677836 3678204 - 0 8 chrY 3677836 3678204 - 0 9 chrY 3677836 3687836 - 0 10 chrY 8370657 8370712 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqq1_k926/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqq1_k926/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcc3hqj55/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcc3hqj55/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq1djyqv_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq1djyqv_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptfn56teq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptfn56teq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 3810063 3811527 + 0 1 chr1 8559398 8562755 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8559398 | 8562755 | a | 0 | ... | | chr1 | 3810063 | 3811527 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 3810063 3811527 + 0 0 chr1 8559398 8562755 + 0 df2 Chromosome Start End Strand Distance 0 chr1 3810063 3811527 + 0 1 chr1 8559398 8562755 + 0 Actual Chromosome Start End Strand Distance 0 chr1 3810063 3811527 + 0 1 chr1 8559398 8562755 + 0 Expected Chromosome Start End Strand Distance 0 chr1 3810063 3811527 + 0 1 chr1 8559398 8562755 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8rs7qgu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8rs7qgu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_og_e1iv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_og_e1iv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu_xub6c_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu_xub6c_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 6991375 6991834 - 0 1 chr1 6991375 6998750 + 0 2 chr1 7417653 7418190 - 0 3 chr1 9871649 9880151 + 0 4 chr16 6991375 7000188 + 0 5 chr21 6991375 7001188 + 0 6 chr5 6991375 6993780 - 0 7 chr6 6991375 6997824 + 0 8 chr7 6991375 7000072 - 0 9 chr8 6991375 6994365 + 0 10 chr9 6991375 7000900 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9871649 | 9880151 | a | 0 | ... | | chr1 | 6991375 | 6998750 | a | 0 | ... | | chr1 | 7417653 | 7418190 | a | 0 | ... | | chr1 | 6991375 | 6991834 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr8 | 6991375 | 6994365 | a | 0 | ... | | chr9 | 6991375 | 7000900 | a | 0 | ... | | chr16 | 6991375 | 7000188 | a | 0 | ... | | chr21 | 6991375 | 7001188 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 8 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr1 6991375 6991834 - 0 4 chr5 6991375 6993780 - 0 7 chr8 6991375 6994365 + 0 5 chr6 6991375 6997824 + 0 1 chr1 6991375 6998750 + 0 6 chr7 6991375 7000072 - 0 9 chr16 6991375 7000188 + 0 8 chr9 6991375 7000900 + 0 10 chr21 6991375 7001188 + 0 2 chr1 7417653 7418190 - 0 0 chr1 9871649 9880151 + 0 df2 Chromosome Start End Strand Distance 0 chr1 6991375 6991834 - 0 6 chr5 6991375 6993780 - 0 9 chr8 6991375 6994365 + 0 7 chr6 6991375 6997824 + 0 1 chr1 6991375 6998750 + 0 8 chr7 6991375 7000072 - 0 4 chr16 6991375 7000188 + 0 10 chr9 6991375 7000900 + 0 5 chr21 6991375 7001188 + 0 2 chr1 7417653 7418190 - 0 3 chr1 9871649 9880151 + 0 Actual Chromosome Start End Strand Distance 0 chr1 6991375 6991834 - 0 1 chr1 6991375 6998750 + 0 2 chr1 7417653 7418190 - 0 3 chr1 9871649 9880151 + 0 4 chr16 6991375 7000188 + 0 5 chr21 6991375 7001188 + 0 6 chr5 6991375 6993780 - 0 7 chr6 6991375 6997824 + 0 8 chr7 6991375 7000072 - 0 9 chr8 6991375 6994365 + 0 10 chr9 6991375 7000900 + 0 Expected Chromosome Start End Strand Distance 0 chr1 6991375 6991834 - 0 1 chr1 6991375 6998750 + 0 2 chr1 7417653 7418190 - 0 3 chr1 9871649 9880151 + 0 4 chr16 6991375 7000188 + 0 5 chr21 6991375 7001188 + 0 6 chr5 6991375 6993780 - 0 7 chr6 6991375 6997824 + 0 8 chr7 6991375 7000072 - 0 9 chr8 6991375 6994365 + 0 10 chr9 6991375 7000900 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb0ch_c04/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb0ch_c04/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4oameqts/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4oameqts/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4l6joh28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4l6joh28/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1062254 1070530 - 0 1 chr1 1940873 1946893 + 0 2 chr1 2608787 2618787 + 0 3 chr1 3792077 3797777 - 0 4 chr1 4176311 4183127 - 0 5 chr1 6753077 6756452 + 0 6 chr1 7298724 7301064 - 0 7 chr13 3477272 3482770 - 0 8 chr16 267307 275583 + 0 9 chr20 2989320 2997328 + 0 10 chr9 941200 946496 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6753077 | 6756452 | a | 0 | ... | | chr1 | 2608787 | 2618787 | a | 0 | ... | | chr1 | 1940873 | 1946893 | a | 0 | ... | | chr1 | 3792077 | 3797777 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 941200 | 946496 | a | 0 | ... | | chr13 | 3477272 | 3482770 | a | 0 | ... | | chr16 | 267307 | 275583 | a | 0 | ... | | chr20 | 2989320 | 2997328 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 11 rows and 12 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 9 chr16 267307 275583 + 0 7 chr9 941200 946496 - 0 5 chr1 1062254 1070530 - 0 2 chr1 1940873 1946893 + 0 1 chr1 2608787 2618787 + 0 10 chr20 2989320 2997328 + 0 8 chr13 3477272 3482770 - 0 3 chr1 3792077 3797777 - 0 6 chr1 4176311 4183127 - 0 0 chr1 6753077 6756452 + 0 4 chr1 7298724 7301064 - 0 df2 Chromosome Start End Strand Distance 8 chr16 267307 275583 + 0 10 chr9 941200 946496 - 0 0 chr1 1062254 1070530 - 0 1 chr1 1940873 1946893 + 0 2 chr1 2608787 2618787 + 0 9 chr20 2989320 2997328 + 0 7 chr13 3477272 3482770 - 0 3 chr1 3792077 3797777 - 0 4 chr1 4176311 4183127 - 0 5 chr1 6753077 6756452 + 0 6 chr1 7298724 7301064 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1062254 1070530 - 0 1 chr1 1940873 1946893 + 0 2 chr1 2608787 2618787 + 0 3 chr1 3792077 3797777 - 0 4 chr1 4176311 4183127 - 0 5 chr1 6753077 6756452 + 0 6 chr1 7298724 7301064 - 0 7 chr13 3477272 3482770 - 0 8 chr16 267307 275583 + 0 9 chr20 2989320 2997328 + 0 10 chr9 941200 946496 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1062254 1070530 - 0 1 chr1 1940873 1946893 + 0 2 chr1 2608787 2618787 + 0 3 chr1 3792077 3797777 - 0 4 chr1 4176311 4183127 - 0 5 chr1 6753077 6756452 + 0 6 chr1 7298724 7301064 - 0 7 chr13 3477272 3482770 - 0 8 chr16 267307 275583 + 0 9 chr20 2989320 2997328 + 0 10 chr9 941200 946496 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=11, step=1) Expected index RangeIndex(start=0, stop=11, step=1) index equal [ True True True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdr9vq27x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdr9vq27x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpts58qto1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpts58qto1/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 7057 - 0 1 chr1 2231971 2235126 - 0 2 chr1 3577292 3586023 + 0 3 chr1 4526443 4533027 + 0 4 chr1 6969854 6972702 - 0 5 chr12 8135147 8143878 + 0 6 chr13 9395130 9396351 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3577292 | 3586023 | a | 0 | ... | | chr1 | 4526443 | 4533027 | a | 0 | ... | | chr1 | 1 | 7057 | a | 0 | ... | | chr1 | 2231971 | 2235126 | a | 0 | ... | | chr1 | 6969854 | 6972702 | a | 0 | ... | | chr12 | 8135147 | 8143878 | a | 0 | ... | | chr13 | 9395130 | 9396351 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 7 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 2 chr1 1 7057 - 0 3 chr1 2231971 2235126 - 0 0 chr1 3577292 3586023 + 0 1 chr1 4526443 4533027 + 0 4 chr1 6969854 6972702 - 0 5 chr12 8135147 8143878 + 0 6 chr13 9395130 9396351 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 7057 - 0 1 chr1 2231971 2235126 - 0 2 chr1 3577292 3586023 + 0 3 chr1 4526443 4533027 + 0 4 chr1 6969854 6972702 - 0 5 chr12 8135147 8143878 + 0 6 chr13 9395130 9396351 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 7057 - 0 1 chr1 2231971 2235126 - 0 2 chr1 3577292 3586023 + 0 3 chr1 4526443 4533027 + 0 4 chr1 6969854 6972702 - 0 5 chr12 8135147 8143878 + 0 6 chr13 9395130 9396351 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 7057 - 0 1 chr1 2231971 2235126 - 0 2 chr1 3577292 3586023 + 0 3 chr1 4526443 4533027 + 0 4 chr1 6969854 6972702 - 0 5 chr12 8135147 8143878 + 0 6 chr13 9395130 9396351 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=7, step=1) Expected index RangeIndex(start=0, stop=7, step=1) index equal [ True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqd94nvd3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd94nvd3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwd7vo8rl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwd7vo8rl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_pry1tkt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_pry1tkt/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 792981 794830 + 0 1 chr1 3306168 3312922 + 0 2 chr1 7588318 7589112 + 0 3 chr1 7761289 7764644 + 0 4 chr1 8974732 8984732 + 0 5 chr10 3259774 3269184 + 0 6 chr10 3761138 3762546 + 0 7 chr9 3564526 3570164 + 0 8 chrX 7423299 7430638 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 3306168 | 3312922 | a | 0 | ... | | chr1 | 792981 | 794830 | a | 0 | ... | | chr1 | 7761289 | 7764644 | a | 0 | ... | | chr1 | 7588318 | 7589112 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr9 | 3564526 | 3570164 | a | 0 | ... | | chr10 | 3259774 | 3269184 | a | 0 | ... | | chr10 | 3761138 | 3762546 | a | 0 | ... | | chrX | 7423299 | 7430638 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 792981 794830 + 0 6 chr10 3259774 3269184 + 0 0 chr1 3306168 3312922 + 0 5 chr9 3564526 3570164 + 0 7 chr10 3761138 3762546 + 0 8 chrX 7423299 7430638 - 0 3 chr1 7588318 7589112 + 0 2 chr1 7761289 7764644 + 0 4 chr1 8974732 8984732 + 0 df2 Chromosome Start End Strand Distance 0 chr1 792981 794830 + 0 5 chr10 3259774 3269184 + 0 1 chr1 3306168 3312922 + 0 7 chr9 3564526 3570164 + 0 6 chr10 3761138 3762546 + 0 8 chrX 7423299 7430638 - 0 2 chr1 7588318 7589112 + 0 3 chr1 7761289 7764644 + 0 4 chr1 8974732 8984732 + 0 Actual Chromosome Start End Strand Distance 0 chr1 792981 794830 + 0 1 chr1 3306168 3312922 + 0 2 chr1 7588318 7589112 + 0 3 chr1 7761289 7764644 + 0 4 chr1 8974732 8984732 + 0 5 chr10 3259774 3269184 + 0 6 chr10 3761138 3762546 + 0 7 chr9 3564526 3570164 + 0 8 chrX 7423299 7430638 - 0 Expected Chromosome Start End Strand Distance 0 chr1 792981 794830 + 0 1 chr1 3306168 3312922 + 0 2 chr1 7588318 7589112 + 0 3 chr1 7761289 7764644 + 0 4 chr1 8974732 8984732 + 0 5 chr10 3259774 3269184 + 0 6 chr10 3761138 3762546 + 0 7 chr9 3564526 3570164 + 0 8 chrX 7423299 7430638 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz3rfs8fu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz3rfs8fu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7refuwc7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7refuwc7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8ltnoxas/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8ltnoxas/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl52dnx08/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl52dnx08/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkw0e7tpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkw0e7tpk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjjpy7fkm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjjpy7fkm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyqfr_rco/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyqfr_rco/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0xs3suu2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0xs3suu2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8a1n7weq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8a1n7weq/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmph1fatqpa/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmph1fatqpa/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1xjt4u4v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1xjt4u4v/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm3nb2ahg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm3nb2ahg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcb_vpbaw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcb_vpbaw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuppo5z7t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuppo5z7t/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxm9tbf8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxm9tbf8_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwyhizxjs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwyhizxjs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8pa0_54x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8pa0_54x/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnj0v3uab/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnj0v3uab/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9z05etx5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9z05etx5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwsiglcca/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwsiglcca/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7lifc7vo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7lifc7vo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3sk9oslq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3sk9oslq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppkro0nfg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppkro0nfg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk41by8b0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk41by8b0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprhbgzjqn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprhbgzjqn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbpxgh3wf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbpxgh3wf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3qu12ybs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3qu12ybs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmploid0j4n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmploid0j4n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2n4ohatl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2n4ohatl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiur_p2dm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiur_p2dm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb3k0syb4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb3k0syb4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfpfapctx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfpfapctx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcon8iacc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcon8iacc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8gvh63za/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8gvh63za/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2vgjnsxe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2vgjnsxe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl_pd3eea/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl_pd3eea/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyapbtdfc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyapbtdfc/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8ilbe1p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8ilbe1p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77s3dg69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77s3dg69/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgpoctgtw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgpoctgtw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4dg7yrbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dg7yrbm/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq8yj88ys/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq8yj88ys/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprln24trp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprln24trp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq2a8379_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2a8379_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi74o40rr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi74o40rr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpel8tpdyw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpel8tpdyw/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0dnyc1s5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0dnyc1s5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbhgofw8u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbhgofw8u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps91j5s28/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps91j5s28/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpguvv260h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpguvv260h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbyfprbs9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbyfprbs9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxg16vlpk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxg16vlpk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptnild05y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptnild05y/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprbnaf6wj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprbnaf6wj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy6zlss59/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy6zlss59/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp215kje6h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp215kje6h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpige3hkp9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpige3hkp9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa4j3g7fe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa4j3g7fe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp75q21gjy/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp75q21gjy/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65546 65804 - 0 1 chr1 65546 65805 - 0 2 chr1 65546 71180 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65546 | 65805 | a | 0 | ... | | chr1 | 65546 | 65804 | a | 0 | ... | | chr1 | 65546 | 71180 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 65546 65804 - 0 0 chr1 65546 65805 - 0 2 chr1 65546 71180 - 0 df2 Chromosome Start End Strand Distance 0 chr1 65546 65804 - 0 1 chr1 65546 65805 - 0 2 chr1 65546 71180 - 0 Actual Chromosome Start End Strand Distance 0 chr1 65546 65804 - 0 1 chr1 65546 65805 - 0 2 chr1 65546 71180 - 0 Expected Chromosome Start End Strand Distance 0 chr1 65546 65804 - 0 1 chr1 65546 65805 - 0 2 chr1 65546 71180 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnt9_1qcp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnt9_1qcp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpp1ak6thw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpp1ak6thw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnxsbamp0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnxsbamp0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnhp8jize/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnhp8jize/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpifwx3z51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpifwx3z51/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 65546 66315 + 0 1 chr1 65546 66315 - 0 2 chr1 65546 66315 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65546 | 66315 | a | 0 | ... | | chr1 | 65546 | 66315 | a | 0 | ... | | chr1 | 65546 | 66315 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 65546 66315 + 0 1 chr1 65546 66315 - 0 2 chr1 65546 66315 - 0 df2 Chromosome Start End Strand Distance 0 chr1 65546 66315 + 0 1 chr1 65546 66315 - 0 2 chr1 65546 66315 - 0 Actual Chromosome Start End Strand Distance 0 chr1 65546 66315 + 0 1 chr1 65546 66315 - 0 2 chr1 65546 66315 - 0 Expected Chromosome Start End Strand Distance 0 chr1 65546 66315 + 0 1 chr1 65546 66315 - 0 2 chr1 65546 66315 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=3, step=1) Expected index RangeIndex(start=0, stop=3, step=1) index equal [ True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgiqb75q3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgiqb75q3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3m5gxuaz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3m5gxuaz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcor32f0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcor32f0u/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp12_znd3n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp12_znd3n/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwebnwgcm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwebnwgcm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnjh875th/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnjh875th/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphh0__k_d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphh0__k_d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0r2k67dp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0r2k67dp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8_g4le8g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_g4le8g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpck3ux2x8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpck3ux2x8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgvpsh536/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgvpsh536/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7udh7t32/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7udh7t32/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmkvbwkyu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmkvbwkyu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjxih1e89/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjxih1e89/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg3iqb24b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg3iqb24b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmywjnrqe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmywjnrqe/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain98-method_chain98] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain169-method_chain169] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. ___________ test_three_in_a_row[strandedness_chain99-method_chain99] ___________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ______________________ test_nearest[downstream-True-same] ______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = True, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=True, E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe41cj5tk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe41cj5tk/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp00o020yp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp00o020yp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc5z_87xx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc5z_87xx/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1929323 1933985 + 0 1 chr1 2920677 2928637 - 0 2 chr1 8542683 8543724 + 0 3 chr12 9010147 9018842 + 0 4 chr7 2 909 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 8542683 | 8543724 | a | 0 | ... | | chr1 | 1929323 | 1933985 | a | 0 | ... | | chr1 | 2920677 | 2928637 | a | 0 | ... | | chr7 | 2 | 909 | a | 0 | ... | | chr12 | 9010147 | 9018842 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 5 rows and 12 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 3 chr7 2 909 - 0 1 chr1 1929323 1933985 + 0 2 chr1 2920677 2928637 - 0 0 chr1 8542683 8543724 + 0 4 chr12 9010147 9018842 + 0 df2 Chromosome Start End Strand Distance 4 chr7 2 909 - 0 0 chr1 1929323 1933985 + 0 1 chr1 2920677 2928637 - 0 2 chr1 8542683 8543724 + 0 3 chr12 9010147 9018842 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1929323 1933985 + 0 1 chr1 2920677 2928637 - 0 2 chr1 8542683 8543724 + 0 3 chr12 9010147 9018842 + 0 4 chr7 2 909 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1929323 1933985 + 0 1 chr1 2920677 2928637 - 0 2 chr1 8542683 8543724 + 0 3 chr12 9010147 9018842 + 0 4 chr7 2 909 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=5, step=1) Expected index RangeIndex(start=0, stop=5, step=1) index equal [ True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptqleufpb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptqleufpb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpilc9kdvl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpilc9kdvl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 2 5984 + 0 1 chr1 372533 377247 - 0 2 chr1 1901373 1910062 - 0 3 chr1 6953395 6959377 + 0 4 chr11 2210609 2215508 - 0 5 chr18 1 2706 + 0 6 chr18 8600730 8605175 - 0 7 chrX 277554 283536 - 0 8 chrX 2228999 2238713 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 6953395 | 6959377 | a | 0 | ... | | chr1 | 2 | 5984 | a | 0 | ... | | chr1 | 372533 | 377247 | a | 0 | ... | | chr1 | 1901373 | 1910062 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr18 | 1 | 2706 | a | 0 | ... | | chr18 | 8600730 | 8605175 | a | 0 | ... | | chrX | 277554 | 283536 | a | 0 | ... | | chrX | 2228999 | 2238713 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 9 rows and 12 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 5 chr18 1 2706 + 0 1 chr1 2 5984 + 0 7 chrX 277554 283536 - 0 2 chr1 372533 377247 - 0 3 chr1 1901373 1910062 - 0 4 chr11 2210609 2215508 - 0 8 chrX 2228999 2238713 - 0 0 chr1 6953395 6959377 + 0 6 chr18 8600730 8605175 - 0 df2 Chromosome Start End Strand Distance 5 chr18 1 2706 + 0 0 chr1 2 5984 + 0 7 chrX 277554 283536 - 0 1 chr1 372533 377247 - 0 2 chr1 1901373 1910062 - 0 4 chr11 2210609 2215508 - 0 8 chrX 2228999 2238713 - 0 3 chr1 6953395 6959377 + 0 6 chr18 8600730 8605175 - 0 Actual Chromosome Start End Strand Distance 0 chr1 2 5984 + 0 1 chr1 372533 377247 - 0 2 chr1 1901373 1910062 - 0 3 chr1 6953395 6959377 + 0 4 chr11 2210609 2215508 - 0 5 chr18 1 2706 + 0 6 chr18 8600730 8605175 - 0 7 chrX 277554 283536 - 0 8 chrX 2228999 2238713 - 0 Expected Chromosome Start End Strand Distance 0 chr1 2 5984 + 0 1 chr1 372533 377247 - 0 2 chr1 1901373 1910062 - 0 3 chr1 6953395 6959377 + 0 4 chr11 2210609 2215508 - 0 5 chr18 1 2706 + 0 6 chr18 8600730 8605175 - 0 7 chrX 277554 283536 - 0 8 chrX 2228999 2238713 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=9, step=1) Expected index RangeIndex(start=0, stop=9, step=1) index equal [ True True True True True True True True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz228w4ga/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz228w4ga/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8_lvi7ku/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8_lvi7ku/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_8a5eji/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_8a5eji/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6gcrrnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6gcrrnu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa9drng6p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa9drng6p/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_fb9_4g_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fb9_4g_/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc_dk_x3f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc_dk_x3f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw08gkmty/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw08gkmty/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwknyrb67/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwknyrb67/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_fplxog9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_fplxog9/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpakw2buto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpakw2buto/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmh7copqg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmh7copqg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6tzaxaai/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6tzaxaai/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpearyr8fd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpearyr8fd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf2kxii51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf2kxii51/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvd1hi_2a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvd1hi_2a/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4w0kqomc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4w0kqomc/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_4gtj9rl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_4gtj9rl/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqiscvpf4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqiscvpf4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdnwnv2nd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdnwnv2nd/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfkftumtu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfkftumtu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpndoaynqp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpndoaynqp/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0etrv8qb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0etrv8qb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvtepona5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvtepona5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe2m_v0dd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe2m_v0dd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9us45t2b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9us45t2b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp77yrqzux/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp77yrqzux/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfay_ec1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfay_ec1j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgltrmjkl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgltrmjkl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9wdf7n2e/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9wdf7n2e/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcaraijtu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcaraijtu/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpy9kq03km/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpy9kq03km/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuwaygcda/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuwaygcda/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp08w6jp68/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp08w6jp68/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpl2y8fdna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpl2y8fdna/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpc2w89j7y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpc2w89j7y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd7ug8j6y/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd7ug8j6y/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpms1l_l10/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpms1l_l10/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpd3d4jzwp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpd3d4jzwp/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfyphfdcr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfyphfdcr/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_lixghs5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_lixghs5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5qqzu0q1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5qqzu0q1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4cmk_wud/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4cmk_wud/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq2qu18f0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq2qu18f0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeo9zcgb0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeo9zcgb0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnl8iz1iz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnl8iz1iz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjhvtwj93/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjhvtwj93/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7s4r3zfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7s4r3zfh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps9p0g09g/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps9p0g09g/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp568ywjmc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp568ywjmc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz57cme4s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz57cme4s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpf772fg1u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpf772fg1u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe9qlsl90/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe9qlsl90/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuzjz5j0u/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuzjz5j0u/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb2z61pu_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb2z61pu_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoumhb6kc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoumhb6kc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa7ekna6j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa7ekna6j/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpijdc5ukz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpijdc5ukz/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2a2fs4qq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2a2fs4qq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgszuan37/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgszuan37/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprn91xjmt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprn91xjmt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqkv2x8cm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqkv2x8cm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvob0uout/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvob0uout/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmkxlgt7w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmkxlgt7w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx8510iup/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx8510iup/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm58zihqb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm58zihqb/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2l89gg_8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2l89gg_8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcb96jhln/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcb96jhln/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiuowqit9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiuowqit9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplndlje5z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplndlje5z/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg42o0cyd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg42o0cyd/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgm96s4_9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgm96s4_9/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpu8x0gr3x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpu8x0gr3x/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphkt9wxk3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphkt9wxk3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnegrthx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnegrthx0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn90gjr51/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn90gjr51/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7_uaxck2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7_uaxck2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain100-method_chain100] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain101-method_chain101] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain102-method_chain102] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain170-method_chain170] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66562 | 66563 | a | 0 | - | E | chr1 | 66562 | 66563 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RkZGRjZGcSYWRgYGRgZGRhZGBnADKBXBCAUmgcAAokAD0=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain103-method_chain103] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ____________________ test_nearest[downstream-True-opposite] ____________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = True, strandedness = 'opposite' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:359: in test_nearest compare_results_nearest(bedtools_df, result) tests/test_binary.py:107: in compare_results_nearest assert_df_equal(result_df, bedtools_df) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ df1 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 = Chromosome Start End Strand Distance 0 chr1 1 2 + 0 def assert_df_equal(df1, df2): print("-"*100) print("df1") print(df1) print("df2") print(df2) # df1.loc[:, "Start"] = df1.Start.astype(np.int64) # df2.loc[:, "Start"] = df1.Start.astype(np.int64) # df1.loc[:, "End"] = df1.End.astype(np.int64) # df2.loc[:, "End"] = df1.End.astype(np.int64) pd.options.mode.chained_assignment = None if "Strand" in df1 and "Strand" in df2: sort_on = "Chromosome Start End Strand".split() df1.Strand = df1.Strand.astype("object") df2.Strand = df2.Strand.astype("object") else: sort_on = "Chromosome Start End".split() if "Strand_b" in df1: sort_on += "Start_b End_b Strand_b".split() df1.Strand_b = df1.Strand_b.astype("object") df2.Strand_b = df2.Strand_b.astype("object") elif "Start_b" in df2: sort_on += "Start_b End_b".split() df1 = df1.sort_values(sort_on) df2 = df2.sort_values(sort_on) df1 = df1.reset_index(drop=True) df2 = df2.reset_index(drop=True) df1.Chromosome = df1.Chromosome.astype("object") df2.Chromosome = df2.Chromosome.astype("object") print("Actual") print(df1.to_csv(sep=" ")) print("Expected") print(df2.to_csv(sep=" ")) print("Actual dtypes") print(df1.dtypes) print("Expected dtypes") print(df2.dtypes) # print("dtypes Strand\n", "1", df1.Strand.dtype, "2", df2.Strand.dtype) # print("dtypes Strand\n", df1.Strand.dtype == df2.Strand.dtype) # print("dtypes equal\n", df1.dtypes == df2.dtypes) print("Actual index") print(df1.index) print("Expected index") print(df2.index) print("index equal", df1.index == df2.index) > pd.testing.assert_frame_equal(df1, df2) E AssertionError: Attributes of DataFrame.iloc[:, 4] (column name="Distance") are different E E Attribute "dtype" are different E [left]: int32 E [right]: int64 E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=True, E strandedness='opposite', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGIEAACLAAY=') as a decorator on your test case tests/helpers.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6th7a4yf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6th7a4yf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxvzxbeko/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxvzxbeko/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp21g0hp1t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp21g0hp1t/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyfc0gwtl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyfc0gwtl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgw_rknte/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgw_rknte/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgyb9bbm_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgyb9bbm_/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp25e5u92r/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp25e5u92r/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpot0zhq4a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpot0zhq4a/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3lzovnlf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3lzovnlf/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoajq78r0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoajq78r0/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2d82sgtv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2d82sgtv/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpneatopoj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpneatopoj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfbkrmksg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfbkrmksg/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9223040 | 9227938 | a | 0 | ... | | chr1 | 9223040 | 9227370 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 9223040 9227370 - 0 0 chr1 9223040 9227938 + 0 df2 Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 Actual Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 Expected Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5st0dxvj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5st0dxvj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplb593rlk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplb593rlk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpq6guy8e6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpq6guy8e6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvqu_r0lr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvqu_r0lr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_egtdps6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_egtdps6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv78y7b8_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv78y7b8_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp15me10e3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp15me10e3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2z89ur3b/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2z89ur3b/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppmk4oaj3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppmk4oaj3/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp36betvxz/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp36betvxz/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppb649bic/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppb649bic/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5gk9_b62/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5gk9_b62/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoj2kvtna/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoj2kvtna/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvl5c6gp5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvl5c6gp5/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqd_lrtms/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqd_lrtms/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1v9anm1j/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1v9anm1j/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpom7944ke/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpom7944ke/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpa46b9pn8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpa46b9pn8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvkdra2a1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvkdra2a1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptb1nampj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptb1nampj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_k57vrdm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_k57vrdm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfpqubp70/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfpqubp70/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzi_r77ww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzi_r77ww/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpiw6i__2n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpiw6i__2n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdol6f8db/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdol6f8db/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt0nz3__c/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt0nz3__c/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk9op3cgt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk9op3cgt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdwls21od/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdwls21od/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 9223040 | 9227938 | a | 0 | ... | | chr1 | 9223040 | 9227370 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 2 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 1 chr1 9223040 9227370 - 0 0 chr1 9223040 9227938 + 0 df2 Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 Actual Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 Expected Chromosome Start End Strand Distance 0 chr1 9223040 9227370 - 0 1 chr1 9223040 9227938 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=2, step=1) Expected index RangeIndex(start=0, stop=2, step=1) index equal [ True True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsfvnrfxw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsfvnrfxw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkcjg3p_2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkcjg3p_2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyg7r9yrb/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyg7r9yrb/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 66818 67084 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66818 | 67084 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 66818 67084 - 0 df2 Chromosome Start End Strand Distance 0 chr1 66818 67084 - 0 Actual Chromosome Start End Strand Distance 0 chr1 66818 67084 - 0 Expected Chromosome Start End Strand Distance 0 chr1 66818 67084 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9jjqiz60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9jjqiz60/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 1 chr1 1128194 1128511 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1128194 | 1128511 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1128194 1128511 + 0 df2 Chromosome Start End Strand Distance 1 chr1 1128194 1128511 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1128194 1128511 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1128194 1128511 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeh6q41r2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeh6q41r2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcxp9kpwn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcxp9kpwn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7ewu9nc1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7ewu9nc1/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvck3gpg3/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvck3gpg3/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4lz4oqgj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4lz4oqgj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjq95hjn_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjq95hjn_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4gbjczxl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4gbjczxl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6spj2ctf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6spj2ctf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpucx9ddt9/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpucx9ddt9/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp8bxpmxol/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp8bxpmxol/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp51gd12jl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp51gd12jl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp88rywcuw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp88rywcuw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm6m_mtdt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm6m_mtdt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqklf3w3t/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqklf3w3t/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmbl8qztd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmbl8qztd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcp7zr_9f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcp7zr_9f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1vrhphch/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1vrhphch/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmf3rudsv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmf3rudsv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpm2ye0wdg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpm2ye0wdg/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7sk197ss/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7sk197ss/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfq62dhbe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfq62dhbe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfr7b6pwt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfr7b6pwt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3_5njb7p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_5njb7p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpsi9gbyy_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpsi9gbyy_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3cr5fxo7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3cr5fxo7/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpfwu3na7v/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpfwu3na7v/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt_a9x6k6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_a9x6k6/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps_fd5ejm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps_fd5ejm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5nkkjikm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5nkkjikm/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5hvd57n0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5hvd57n0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmo0k961l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmo0k961l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn9qrxtc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn9qrxtc2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk0ur7v61/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk0ur7v61/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps5aj8rmw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps5aj8rmw/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 1282 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 1282 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw_p0jdq2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw_p0jdq2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpppk3e0rm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpppk3e0rm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpncrc7mzo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpncrc7mzo/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 3 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 3 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 3 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppw33x4ny/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppw33x4ny/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpn4tg8cot/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpn4tg8cot/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpoefaptw2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpoefaptw2/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpr0md6qnu/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpr0md6qnu/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpb4f61mfl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpb4f61mfl/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmphgjo2og4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmphgjo2og4/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbt_vdr69/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbt_vdr69/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwv8r0amn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwv8r0amn/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdf_f22er/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdf_f22er/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0utvans1/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0utvans1/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4ud8p3ky/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4ud8p3ky/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyg2_vaoc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyg2_vaoc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzdw2sjvs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzdw2sjvs/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 - 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 - 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] cmd cmd cmd cmd cmd bedtools closest -iu -D a -S -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt80axrac/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt80axrac/f2.bed) bedtools bedtools bedtools bedtools bedtools Chromosome Start End Strand Distance 0 chr1 1 2 + 0 result result result result result +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ---------------------------------------------------------------------------------------------------- df1 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 df2 Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Expected Chromosome Start End Strand Distance 0 chr1 1 2 + 0 Actual dtypes Chromosome object Start int64 End int64 Strand object Distance int32 dtype: object Expected dtypes Chromosome object Start int64 End int64 Strand object Distance int64 dtype: object Actual index RangeIndex(start=0, stop=1, step=1) Expected index RangeIndex(start=0, stop=1, step=1) index equal [ True] ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain145-method_chain145] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain104-method_chain104] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain105-method_chain105] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain171-method_chain171] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65537 | 65539 | a | 0 | - | E | chr2 | 65537 | 65911 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66818 | 67075 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RgZ2RgYQQBBhBiAFNA7MhYysAA5jEyQ4RBoqwQZQzMQAySZUgHSwEAKsQBVg==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. _____________________ test_nearest[downstream-False-False] _____________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = False, strandedness = False @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:115: in _nearest r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, pyranges/methods/nearest.py:62: in _next_nonoverlapping r_idx, dist = nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=False, E strandedness=False, E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:34: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkw1leus7/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkw1leus7/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp61n5epzr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp61n5epzr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6c0s3m2q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6c0s3m2q/f2.bed) bedtools bedtools bedtools bedtools bedtools Empty DataFrame Columns: [Chromosome, Start, End, Strand, Distance] Index: [] result result result result result Empty PyRanges cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmppbulsfww/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmppbulsfww/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz8ehcunm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz8ehcunm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpno_l_2dp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpno_l_2dp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe8gi1hq8/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe8gi1hq8/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmagocmb2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmagocmb2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpadhllvej/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpadhllvej/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3_7llt4z/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3_7llt4z/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvsvnoz5q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvsvnoz5q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgeyhd8bf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgeyhd8bf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7gff77vr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7gff77vr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3vpnoawg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3vpnoawg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp92ck7y5a/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp92ck7y5a/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4on33ars/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4on33ars/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4zqse6i4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4zqse6i4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0llr19kw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0llr19kw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxwx78b8k/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxwx78b8k/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6r1jfkdq/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6r1jfkdq/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdbpq61ir/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdbpq61ir/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_w5o1svk/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_w5o1svk/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmprv8x93zg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmprv8x93zg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpdanql897/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpdanql897/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpphxa8jbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpphxa8jbm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjh6qej3s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjh6qej3s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9xvjtjvo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9xvjtjvo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmplcnfr_sj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmplcnfr_sj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5b2mgv7_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5b2mgv7_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4imhk2hs/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4imhk2hs/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp83b_y233/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp83b_y233/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpt_fxypum/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpt_fxypum/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmps6mosygt/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmps6mosygt/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpyuod7m9s/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpyuod7m9s/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3gnxkfbm/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3gnxkfbm/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptor1hnkc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptor1hnkc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg8nbfo83/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg8nbfo83/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwe1gi5mp/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwe1gi5mp/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp5jgonq5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp5jgonq5p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_ddd9gsw/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_ddd9gsw/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9k4od41f/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9k4od41f/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpg5d7lsit/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpg5d7lsit/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6yulugns/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6yulugns/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpkima79o0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpkima79o0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4dlw_meh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4dlw_meh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpewvdmqph/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpewvdmqph/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbb2ezuzl/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbb2ezuzl/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnytlo7f5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnytlo7f5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpjbk42d72/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpjbk42d72/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk6stlt80/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk6stlt80/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp76ue9egj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp76ue9egj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpmxgnqrfh/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpmxgnqrfh/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqr0i3a7x/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqr0i3a7x/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpqh8b5n5p/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpqh8b5n5p/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpe0s8rli4/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpe0s8rli4/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp_o66vxsx/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp_o66vxsx/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp4xwfunub/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp4xwfunub/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpuci_jdeg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpuci_jdeg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp7fxf5da2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp7fxf5da2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxq2geqg5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxq2geqg5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpx7_xt1h5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpx7_xt1h5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpvc5quvx0/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpvc5quvx0/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgbd3q47n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgbd3q47n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpeutzoxc2/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpeutzoxc2/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcs75goi_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcs75goi_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpk80pq3a_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpk80pq3a_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpv9k8eocf/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpv9k8eocf/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ifwr4ff/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ifwr4ff/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpupkpm7tj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpupkpm7tj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgxiv58k_/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgxiv58k_/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp9tp2lgto/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp9tp2lgto/f2.bed) ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain106-method_chain106] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain147-method_chain147] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') _____________________ test_nearest[downstream-False-same] ______________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 nearest_how = 'downstream', overlap = False, strandedness = 'same' @pytest.mark.bedtools > @pytest.mark.parametrize("nearest_how,overlap,strandedness", product(nearest_hows, overlaps, strandedness)) tests/test_binary.py:323: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_binary.py:351: in test_nearest result = gr.nearest( pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:115: in _nearest r_idx, dist = _next_nonoverlapping(df_to_find_nearest_in.End, pyranges/methods/nearest.py:62: in _next_nonoverlapping r_idx, dist = nearest_next_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_nearest( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E nearest_how='downstream', E overlap=False, E strandedness='same', E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEFAIAAIoABQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:34: ValueError ----------------------------- Captured stdout call ----------------------------- cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpcepf3h9w/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpcepf3h9w/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpzuxcx7wv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpzuxcx7wv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp54jhq8kr/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp54jhq8kr/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpugt5btf6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpugt5btf6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp0g4j1q60/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp0g4j1q60/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpnppra6tj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpnppra6tj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3s1tdo9h/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3s1tdo9h/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpwqnp0uof/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpwqnp0uof/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpw79ds6c6/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpw79ds6c6/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpczc85mpe/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpczc85mpe/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpbeqk7u2m/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpbeqk7u2m/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi8nueg7l/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi8nueg7l/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptpmvtaak/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptpmvtaak/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp064nkm6n/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp064nkm6n/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp1e4uhvfd/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp1e4uhvfd/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpxyu3yw1q/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpxyu3yw1q/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptx1aqehv/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptx1aqehv/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpgtp84bye/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpgtp84bye/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpi5tbn0yn/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpi5tbn0yn/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp42v1o9oo/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp42v1o9oo/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmpz0itdljg/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmpz0itdljg/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp3ifybjf5/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp3ifybjf5/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp95bmsfyc/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp95bmsfyc/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp6qfxrb1d/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp6qfxrb1d/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmptbodghtj/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmptbodghtj/f2.bed) cmd cmd cmd cmd cmd bedtools closest -iu -D a -s -io -t first -d -a <(sort -k1,1 -k2,2n /tmp/tmp2wtsy3ta/f1.bed) -b <(sort -k1,1 -k2,2n /tmp/tmp2wtsy3ta/f2.bed) __________ test_three_in_a_row[strandedness_chain107-method_chain107] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain148-method_chain148] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain108-method_chain108] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain172-method_chain172] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGCEkowQFiMDnA8FAAEnAAo=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain149-method_chain149] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain109-method_chain109] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain150-method_chain150] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain196-method_chain196] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain110-method_chain110] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain151-method_chain151] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain197-method_chain197] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain111-method_chain111] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', 'opposite'), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain152-method_chain152] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain198-method_chain198] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain173-method_chain173] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain153-method_chain153] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain199-method_chain199] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain154-method_chain154] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain112-method_chain112] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain200-method_chain200] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain155-method_chain155] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain174-method_chain174] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65798 | 65800 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RkZGBkACIWRkZWIAXmAgVAAEqhAwADnwAX') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain201-method_chain201] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain156-method_chain156] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain113-method_chain113] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain202-method_chain202] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same'), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain157-method_chain157] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain203-method_chain203] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain175-method_chain175] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain204-method_chain204] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain205-method_chain205] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain176-method_chain176] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain206-method_chain206] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain229-method_chain229] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain115-method_chain115] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', 'opposite'), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 371457 | 371714 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 371457 | 371714 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 258 | 515 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', 'opposite'), E method_chain=('overlap', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RghEIGVtbVDAwgBgOjnX7HMagwVBQsHCDCWMsAEQcJgMUAk8gEHA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain207-method_chain207] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain256-method_chain256] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain208-method_chain208] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain257-method_chain257] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain209-method_chain209] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain231-method_chain231] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain258-method_chain258] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain232-method_chain232] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain178-method_chain178] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 678658 | 679683 | a | 0 | - | E | chr1 | 582009 | 583034 | a | 0 | - | E | chr1 | 2 | 1027 | a | 0 | - | E | chr1 | 2476210 | 2477235 | a | 0 | - | E | chr1 | 9315423 | 9316448 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 787 | a | 0 | + | E | chr1 | 473601 | 475906 | a | 0 | + | E | chr1 | 1 | 2306 | a | 0 | + | E | chr1 | 1 | 2306 | a | 0 | + | E | chr1 | 1 | 2306 | a | 0 | + | E | chr1 | 1 | 2306 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 786691 | 786948 | a | 0 | + | E | chr1 | 786691 | 786695 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicYwxteXKV0c/L8hFjqNVyB8Y0p8PPGZX55/QwMLIwMjAysvD0qcQxMqpyPKxgZA5SPbGRkamOASjOEMYVzQhksIA5jOYJ7AyMnkpGbIxGZZKVjIrJavcY1eLqDRkDI6YbApWwMzIyslsxsIHUMgD5DIzMggyanCAmo43EYXbGcq1VnSBxBh5GJqDFwYwMrEAtDMxAFQC4yhoL') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain259-method_chain259] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain210-method_chain210] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain233-method_chain233] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain211-method_chain211] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain260-method_chain260] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkYEyexAACjAzIFBgAABjFAPo=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain180-method_chain180] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain234-method_chain234] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain182-method_chain182] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain183-method_chain183] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain235-method_chain235] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain262-method_chain262] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65795 | 65797 | a | 0 | + | E | chr1 | 65795 | 72496 | a | 0 | + | E | chr1 | 65795 | 66309 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66818 | 67075 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131330 | 131587 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RkZZRkLGBnYmQsZGdnZmBkYGRkYgRTcJrR0kxKhwHEhfAhFCuIYGADqwGZAdUNEgGZxsAOVgcWAgCmEAJT') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain184-method_chain184] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain215-method_chain215] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain236-method_chain236] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain264-method_chain264] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain185-method_chain185] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 257 | 585 | a | 0 | ... | | chr1 | 257 | 1027 | a | 0 | ... | | chr1 | 257 | 819 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain237-method_chain237] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same'), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain186-method_chain186] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 65586 | 65592 | a | 0 | + | | chr1 | 65586 | 65592 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain238-method_chain238] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain217-method_chain217] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain266-method_chain266] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain187-method_chain187] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain239-method_chain239] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain218-method_chain218] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain267-method_chain267] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | - | E | chr1 | 1 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkYGCoYmBgZGRgFGpdEs2YLrjyOpgLBnCKEQBomgQT') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain188-method_chain188] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', False), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain219-method_chain219] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 98088 | 104586 | a | 0 | - | E | chr1 | 98088 | 98089 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 4098 | 4099 | a | 0 | + | E | chr1 | 4098 | 4099 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY5RhqQtjVGJkZGQAYSBgZKxXZ2SwlUxkYATzbBjlJBlLIhnFgBwgFAARECmoAiACALiLA/Y=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain268-method_chain268] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 327937 | 328963 | a | 0 | + | E | chr1 | 327937 | 328963 | a | 0 | + | E | chr1 | 327937 | 328963 | a | 0 | + | E | chr1 | 327937 | 328963 | a | 0 | + | E | chr1 | 327937 | 328963 | a | 0 | + | E | chr22 | 327937 | 328963 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65552 | 65809 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY/Rg3d/GGKz1/zRjlHpCC2O0VdNiRjGtkjZG/ZjFPxkYGRhBgImRkZmRkYVBlJGVkYFBDUQwsoAIoDQDlOIH80FsCA1kMDMCAE0aCuI=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain189-method_chain189] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain220-method_chain220] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 5569537 | 5569795 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66050 | 66051 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY+RgYGQAIiBhFvIHyGIEcRnZ2SGijExgKQY4ycgIAD5XAbQ=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain269-method_chain269] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 97793 | 98110 | a | 0 | - | E | chr2 | 74334 | 74848 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131078 | 131350 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicYwxzZLzGyACC7IwMDECKixHCZWSsA3IZlWIZGVmYgGLMjDYgURCTgZGFEUixgpQxsDMxsALV8YM1MzKImwMJAMg5A1o=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain190-method_chain190] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAEECwEAAFEAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain243-method_chain243] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same'), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain221-method_chain221] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 259 | a | 0 | - | E | chr1 | 852075 | 852332 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 259 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY+RsjPnGGOP1s4uBgZGRgQFEMkryMmQxMHAAuYxMQC5ImJGXkYEFSDFwMjLEAgWYwWpBEmw+pUxsjAA5BAX+') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain270-method_chain270] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7240513 | 7245544 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 9822733 | 9822734 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY8wNcy5jYARD47xqByBVKLwMSDIwMNpIPVQAUowMTFMf8YBU6DEzgMQhsgzSyYwAIBMHnQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain222-method_chain222] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7777574 | 7778090 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AAABZpM91mYTPQAAAVVxpXYAAAEAEXatJQABAgMAAA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain245-method_chain245] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain271-method_chain271] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr15 | 1966339 | 1968135 | a | 0 | - | E | chr15 | 67842 | 69638 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr2 | 2306 | 2563 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicJYcxCsAgEMASCxYpdHWrU//iYH/ne4sHhgwJ1vm/LYPdrMNvALdBER8TnAexV6Rsyw4WuCgDlA==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain246-method_chain246] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain223-method_chain223] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same'), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 67074 | 67331 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 66050 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'same'), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY3RgZGBkACJGRjZGBjEgE8hiBFMMYJoRJA/iAwE7WAwAE3cAfA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain247-method_chain247] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain272-method_chain272] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2849197 | 2849393 | a | 0 | + | E | chr13 | 68610 | 68806 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1310978 | 1311237 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicYxQTMKhgVGn7K8LAyMDIyMjAA6Q1tSvXMDJmMfIwMjC4MxwGkkApEALSDMEiQAYbIxNIfQLPFwZGFkZGADbxB3s=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain248-method_chain248] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain194-method_chain194] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', False), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 259 | 261 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', False), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AAAAAAE+EQACAQ0AAAEGbGkbAAABAA4AAQIAAAABAAE=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain224-method_chain224] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2CAAkZGBkYoiwEBAABpAAU=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain249-method_chain249] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain273-method_chain273] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain281-method_chain281] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain250-method_chain250] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain251-method_chain251] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain225-method_chain225] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'same') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'same'), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain274-method_chain274] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain282-method_chain282] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain252-method_chain252] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain253-method_chain253] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain254-method_chain254] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain255-method_chain255] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain283-method_chain283] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain303-method_chain303] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain304-method_chain304] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain322-method_chain322] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain284-method_chain284] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain305-method_chain305] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain276-method_chain276] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGDEEGJEloZKMAIAAR8ACQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 1 | 2 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain306-method_chain306] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain323-method_chain323] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain307-method_chain307] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain285-method_chain285] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain286-method_chain286] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain278-method_chain278] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain308-method_chain308] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain280-method_chain280] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain309-method_chain309] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain287-method_chain287] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain327-method_chain327] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 341 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 341 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 341 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 260 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 259 | a | 0 | - | | chr1 | 258 | 259 | a | 0 | - | | chr1 | 258 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 259 | a | 0 | - | | chr1 | 258 | 259 | a | 0 | - | | chr1 | 258 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 341 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 515 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 515 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 342 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 258 | 259 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 340 | 517 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain288-method_chain288] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain339-method_chain339] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65583 | 65841 | a | 0 | - | E | chr1 | 65583 | 65841 | a | 0 | - | E | chr1 | 67090 | 69490 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 69380 | 73491 | a | 0 | + | E | chr1 | 69380 | 73491 | a | 0 | + | E | chr1 | 69380 | 73491 | a | 0 | + | E | chr1 | 69380 | 73491 | a | 0 | + | E | chr1 | 69380 | 73491 | a | 0 | + | E | chr1 | 69380 | 73491 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 6 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 66050 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('join', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RjZGJkZGQAQhCDAUKxCQIZDHpAJmc8SAiIrDPZGBl5zaPYGYMj/09jjO1/q8xoxc7IDlTDzghRzc/MIC/Ax8jCwMjMwMjKwMjEwAg2kZOBkY0BbAXYLAYGbhABAP7AB20=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +12 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | ... | ... | ... | ... | ... | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | | chr1 | 67090 | 69490 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 10 rows and 17 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 12 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Start_c, ... (+ 5 more.) ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain329-method_chain329] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain330-method_chain330] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain311-method_chain311] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 3 | a | 0 | - | E | chr1 | 1 | 3 | a | 0 | - | E | chr16 | 10000000 | 10000002 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 259 | a | 0 | - | E | chr1 | 1 | 259 | a | 0 | - | E | chr1 | 2110978 | 2111238 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 131336 | 137195 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('overlap', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RgYGBiBBKMIAJIgZmMjEwM/AxQETDFyFQ7Y1o9SB7IZ4QIYtXHiKKNgUHBDCjozsgMkoVgJrApTIzsDBxijxgYAebcBB4=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain341-method_chain341] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain331-method_chain331] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain292-method_chain292] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', 'opposite') method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', 'opposite'), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain343-method_chain343] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain332-method_chain332] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain313-method_chain313] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain344-method_chain344] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain345-method_chain345] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain294-method_chain294] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain333-method_chain333] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain346-method_chain346] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain295-method_chain295] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain347-method_chain347] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain296-method_chain296] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain348-method_chain348] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain297-method_chain297] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain334-method_chain334] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain349-method_chain349] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain298-method_chain298] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain315-method_chain315] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain350-method_chain350] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain299-method_chain299] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain351-method_chain351] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain300-method_chain300] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain335-method_chain335] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain352-method_chain352] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain301-method_chain301] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain353-method_chain353] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain302-method_chain302] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain336-method_chain336] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain316-method_chain316] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain354-method_chain354] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain355-method_chain355] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain337-method_chain337] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain356-method_chain356] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain367-method_chain367] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0Y4gU6hcQAA6QAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain317-method_chain317] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0Y4gU6hcQAA6QAH') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain378-method_chain378] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain357-method_chain357] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain379-method_chain379] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain368-method_chain368] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3073 | 8194 | a | 0 | + | E | chr1 | 3073 | 8194 | a | 0 | + | E | chr1 | 3073 | 8194 | a | 0 | + | E | chr1 | 3073 | 8194 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2SvtHBkYGBkYAARfBAWo63eMz5Gt86ELMZEB+ZfjMXykkcYGJkZwZI8QCzCAAWMjCAdACrbBz4=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain318-method_chain318] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 196609 | 199682 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65610 | 65867 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RkEGRkYGBkYGRmYGCQ4QEyGaU9cirAQowMniCaAUwwAgEDIwAwdQHe') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain358-method_chain358] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain380-method_chain380] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain369-method_chain369] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain319-method_chain319] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65538 | 65539 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY+QJifjCwMDIgACMyExkCQgHAE7lAbM=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain381-method_chain381] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain382-method_chain382] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain370-method_chain370] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGOGBkRBJihDLh8gAA/wAJ') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain320-method_chain320] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=(False, None), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain360-method_chain360] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('overlap', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66562 | 67844 | a | 0 | - | E | chr1 | 66562 | 67076 | a | 0 | - | E | chr1 | 66562 | 66564 | a | 0 | - | E | chr2 | 66562 | 67076 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66306 | 66564 | a | 0 | + | E | chr1 | 66306 | 66564 | a | 0 | + | E | chr1 | 66306 | 67332 | a | 0 | - | E | chr1 | 66306 | 66564 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 6 | 3592 | a | 0 | + | E | chr1 | 6 | 3592 | a | 0 | + | E | chr1 | 6 | 3592 | a | 0 | + | E | chr1 | 6 | 3592 | a | 0 | + | E | chr1 | 6 | 3592 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 5 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('overlap', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicPY3BCcJAEEX/200IKCgeVMhBsQAPgjbgxYOn1JBbOrAQO7CYlOWfQVyW/czMm7eI2xqe+4lucfowch9EoQc2VCHiNG7FraCjK2eUHCiPJERL7NUcxVbq+vcw+oPXZO15DnJpaBuAStos+wsyxU9RTHb2cGF3bRKR8mmlleMLU5oJ0g==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ('overlap', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 65794 | 66564 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 1 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') Empty PyRanges ('overlap', 'nearest') ('overlap', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain383-method_chain383] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain371-method_chain371] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain384-method_chain384] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') __________ test_three_in_a_row[strandedness_chain321-method_chain321] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = (False, None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=(False, None), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAAUYGKGDERqFxAADzAAc=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain372-method_chain372] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain362-method_chain362] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain385-method_chain385] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') __________ test_three_in_a_row[strandedness_chain386-method_chain386] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain388-method_chain388] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('join', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:68: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2, suffix="_c") pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65535 | 65537 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65536 | 65537 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('join', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0Yg/v8PwmBkYEAS/I/EYUCSBAIAmHkEAw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges 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'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ('join', 'nearest') Empty PyRanges ('join', 'nearest') Empty PyRanges ('join', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain396-method_chain396] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_union', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') Empty PyRanges ('set_union', 'intersect') __________ test_three_in_a_row[strandedness_chain374-method_chain374] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66817 | 67083 | a | 0 | - | E | chr1 | 1245445 | 1245711 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66901 | 67159 | a | 0 | - | E | chr1 | 5506442 | 5506700 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 258 | 527 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY+QWXvGBMV1hiTwDAyMjELEyMDAIM7IwcDByMoIF2IEUIweDJBcDIwgyMnAzsoYwMrKEsHYC+UIgWaASBgYYBYQMbBCzeBgYAGXBBQU=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain364-method_chain364] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain397-method_chain397] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('set_union', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') Empty PyRanges ('set_union', 'subtract') __________ test_three_in_a_row[strandedness_chain398-method_chain398] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_union', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') Empty PyRanges ('set_union', 'join') __________ test_three_in_a_row[strandedness_chain390-method_chain390] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain399-method_chain399] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') Empty PyRanges ('set_intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain400-method_chain400] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') Empty PyRanges ('set_intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain365-method_chain365] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain401-method_chain401] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') ('set_intersect', 'overlap') ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') Empty PyRanges ('set_intersect', 'overlap') __________ test_three_in_a_row[strandedness_chain376-method_chain376] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('same', None), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain392-method_chain392] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') Empty PyRanges ('set_union', 'set_union') __________ test_three_in_a_row[strandedness_chain402-method_chain402] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') Empty PyRanges ('set_intersect', 'nearest') __________ test_three_in_a_row[strandedness_chain393-method_chain393] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_union', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('set_union', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') Empty PyRanges ('set_union', 'set_intersect') __________ test_three_in_a_row[strandedness_chain394-method_chain394] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_union', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') Empty PyRanges ('set_union', 'overlap') __________ test_three_in_a_row[strandedness_chain366-method_chain366] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('same', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('same', None), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBGBEohgZ0OQBANYABw==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain395-method_chain395] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('set_union', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_union', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') Empty PyRanges ('set_union', 'nearest') __________ test_three_in_a_row[strandedness_chain403-method_chain403] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') Empty PyRanges ('set_intersect', 'intersect') __________ test_three_in_a_row[strandedness_chain411-method_chain411] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('overlap', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') Empty PyRanges ('overlap', 'subtract') __________ test_three_in_a_row[strandedness_chain416-method_chain416] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65794 | 65797 | a | 0 | + | E | chr1 | 65794 | 65797 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('nearest', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2JkAAImRga5oO0MjGDIwMjIyMAEEgMy2cEUiMWAFQAAQpYBRQ==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') Empty PyRanges ('nearest', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain404-method_chain404] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') Empty PyRanges ('set_intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain421-method_chain421] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') Empty PyRanges ('intersect', 'set_intersect') __________ test_three_in_a_row[strandedness_chain405-method_chain405] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('set_intersect', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('set_intersect', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') Empty PyRanges ('set_intersect', 'join') __________ test_three_in_a_row[strandedness_chain406-method_chain406] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('overlap', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') ('overlap', 'set_union') Empty PyRanges ('overlap', 'set_union') __________ test_three_in_a_row[strandedness_chain417-method_chain417] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 2 | 3 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('nearest', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2TABIyYHEaEIAAApwAG') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') Empty PyRanges ('nearest', 'intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain413-method_chain413] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('nearest', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') Empty PyRanges ('nearest', 'set_union') ('nearest', 'set_union') ('nearest', 'set_union') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain423-method_chain423] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('intersect', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 3936561 | 3936824 | a | 0 | + | E | chr1 | 65539 | 67077 | a | 0 | + | E | chr1 | 65539 | 67077 | a | 0 | + | E | chr1 | 65539 | 65796 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 66818 | 69892 | a | 0 | - | E | chr1 | 66818 | 71684 | a | 0 | - | E | chr1 | 66818 | 69892 | a | 0 | - | E | chr1 | 66818 | 69892 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 65793 | 65795 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('intersect', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicNY29DcJQDITve3n4CREpQhmAPlUqKiQWYIwsEHo2YDdWoKanx4cUuzjr/sz99nm2wnC6njuE9qj/ThJofT+Wy3HWARU6WYWQAsv/8RF1aAEjxYYwa+PO+mgQPVmQWJOKV4ZafnG6om1/dh4IfA==') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 68334 | a | 0 | ... | | chr1 | 66590 | 68114 | a | 0 | ... | | chr1 | 66590 | 68334 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 68334 | a | 0 | ... | | chr1 | 66590 | 68114 | a | 0 | ... | | chr1 | 66590 | 68334 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 68334 | a | 0 | ... | | chr1 | 66590 | 68114 | a | 0 | ... | | chr1 | 66590 | 68334 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 66592 | a | 0 | ... | | chr1 | 66590 | 66592 | a | 0 | ... | | chr1 | 66590 | 66592 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 68334 | a | 0 | ... | | chr1 | 66590 | 68114 | a | 0 | ... | | chr1 | 66590 | 68334 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 67359 | a | 0 | ... | | chr1 | 66590 | 67359 | a | 0 | ... | | chr1 | 66590 | 67359 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 66592 | a | 0 | ... | | chr1 | 66590 | 66592 | a | 0 | ... | | chr1 | 66590 | 66592 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 73539 | a | 0 | ... | | chr1 | 66590 | 68114 | a | 0 | ... | | chr1 | 66590 | 68618 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 68334 | a | 0 | ... | | chr1 | 66590 | 68114 | a | 0 | ... | | chr1 | 66590 | 68334 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') +--------------+-----------+-----------+------------+-----------+-------+ | Chromosome | Start | End | Name | Score | +7 | | (category) | (int64) | (int64) | (object) | (int64) | ... | |--------------+-----------+-----------+------------+-----------+-------| | chr1 | 66590 | 67359 | a | 0 | ... | | chr1 | 66590 | 67359 | a | 0 | ... | | chr1 | 66590 | 67359 | a | 0 | ... | +--------------+-----------+-----------+------------+-----------+-------+ Stranded PyRanges object has 3 rows and 12 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. 7 hidden columns: Strand, Start_b, End_b, Name_b, Score_b, Strand_b, Distance ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') Empty PyRanges ('intersect', 'nearest') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain407-method_chain407] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('overlap', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('overlap', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') Empty PyRanges ('overlap', 'set_intersect') __________ test_three_in_a_row[strandedness_chain418-method_chain418] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('nearest', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') Empty PyRanges ('nearest', 'subtract') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain414-method_chain414] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('nearest', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('nearest', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') Empty PyRanges ('nearest', 'set_intersect') ('nearest', 'set_intersect') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain425-method_chain425] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('intersect', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') Empty PyRanges ('intersect', 'subtract') __________ test_three_in_a_row[strandedness_chain419-method_chain419] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:63: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 514 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 7012609 | 7012866 | a | 0 | + | E | chr1 | 7012609 | 7012866 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('nearest', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2RkZIBAJkYGTSDFwMAFJBjBwqxAAiTCyBCYDaERBCMjABtXAQ4=') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') ('nearest', 'join') Empty PyRanges ('nearest', 'join') Empty PyRanges ('nearest', 'join') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain427-method_chain427] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') Empty PyRanges ('subtract', 'set_union') __________ test_three_in_a_row[strandedness_chain429-method_chain429] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('subtract', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') Empty PyRanges ('subtract', 'overlap') __________ test_three_in_a_row[strandedness_chain415-method_chain415] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('nearest', 'overlap') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:3023: in nearest dfs = pyrange_apply(_nearest, self, other, **kwargs) pyranges/multithreaded.py:235: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/methods/nearest.py:121: in _nearest previous_r_idx, previous_dist = _previous_nonoverlapping( pyranges/methods/nearest.py:74: in _previous_nonoverlapping r_idx, dist = nearest_previous_nonoverlapping( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' E Falsifying example: test_three_in_a_row( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 590082 | 592388 | a | 0 | - | E | chr1 | 2 | 2308 | a | 0 | - | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 257 | 771 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('nearest', 'overlap'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY1SVeCHImKLf5c3AwMjIwMAJJIAUmAUUAAkxgESYGcEUEDCBSQaGmhnT6tX5GACvPgUn') as a decorator on your test case sorted_nearest/src/sorted_nearest.pyx:24: ValueError ----------------------------- Captured stdout call ----------------------------- ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') Empty PyRanges ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ('nearest', 'overlap') ---------------------------------- Hypothesis ---------------------------------- WARNING: Hypothesis has spent more than five minutes working to shrink a failing example, and stopped because it is making very slow progress. When you re-run your tests, shrinking will resume and may take this long before aborting again. PLEASE REPORT THIS if you can provide a reproducing example, so that we can improve shrinking performance for everyone. __________ test_three_in_a_row[strandedness_chain428-method_chain428] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('subtract', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') Empty PyRanges ('subtract', 'set_intersect') __________ test_three_in_a_row[strandedness_chain420-method_chain420] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('intersect', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('intersect', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') Empty PyRanges ('intersect', 'set_union') __________ test_three_in_a_row[strandedness_chain430-method_chain430] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'nearest') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('subtract', 'nearest'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') Empty PyRanges ('subtract', 'nearest') __________ test_three_in_a_row[strandedness_chain432-method_chain432] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('subtract', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 1966340 | 1966597 | a | 0 | - | | chr21 | 1966340 | 1966597 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 1966340 | 1966597 | a | 0 | - | | chr21 | 1966340 | 1966597 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 1966340 | 1966597 | a | 0 | - | | chr21 | 1966340 | 1966597 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 1966340 | 1966597 | a | 0 | - | | chr21 | 1966340 | 1966597 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 2 | 259 | a | 0 | + | | chr21 | 2294020 | 2294278 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 2 | 4611 | a | 0 | + | | chr21 | 2 | 8964 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr9 | 2 | 4611 | a | 0 | + | | chr21 | 2 | 8964 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2294020 | 2294278 | a | 0 | + | | chr9 | 2 | 259 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 260 | 518 | a | 0 | + | | chr9 | 66305 | 66562 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1966340 | 1966598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1966340 | 1966598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1966340 | 1966598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1966340 | 1966598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1966340 | 1966598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr21 | 1966340 | 1966598 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') Empty PyRanges ('subtract', 'subtract') __________ test_three_in_a_row[strandedness_chain435-method_chain435] __________ [gw1] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('join', 'set_intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3688: in set_intersect other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('join', 'set_intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') Empty PyRanges ('join', 'set_intersect') __________ test_three_in_a_row[strandedness_chain431-method_chain431] __________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None) method_chain = ('subtract', 'intersect') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('subtract', 'intersect'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') Empty PyRanges ('subtract', 'intersect') __________ test_three_in_a_row[strandedness_chain439-method_chain439] __________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('join', 'subtract') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('join', 'subtract'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') ('join', 'subtract') ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') Empty PyRanges ('join', 'subtract') __________ test_three_in_a_row[strandedness_chain433-method_chain433] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('subtract', 'join') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:77: in test_three_in_a_row gr2 = m1(gr2, strandedness=s1) pyranges/pyranges.py:4384: in subtract other_clusters = other.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E gr3=Empty PyRanges, E strandedness_chain=('opposite', None), E method_chain=('subtract', 'join'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAJGFAoCAABcAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') Empty PyRanges ('subtract', 'join') _______________________________ test_merge[True] _______________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strand=True, E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpxr6om8e6/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 660493 | 667247 | a | 0 | - | | chr1 | 5975919 | 5980020 | a | 0 | - | | chr1 | 4509450 | 4514671 | a | 0 | - | | chr1 | 4718231 | 4726120 | a | 0 | - | | chr3 | 8666068 | 8674604 | a | 0 | - | | chr4 | 7123814 | 7124735 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpef3nova3/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 660493 667247 - 1 chr1 4509450 4514671 - 1 chr1 4718231 4726120 - 1 chr1 5975919 5980020 - 1 chr3 8666068 8674604 - 1 chr4 7123814 7124735 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 660493 667247 - 1 1 chr1 4509450 4514671 - 1 2 chr1 4718231 4726120 - 1 3 chr1 5975919 5980020 - 1 4 chr3 8666068 8674604 - 1 5 chr4 7123814 7124735 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7616546 | 7622325 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpu9grrc_0/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7616546 7622325 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 7616546 7622325 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5924745 | 5929982 | a | 0 | + | | chr1 | 7347229 | 7349479 | a | 0 | + | | chr1 | 4323803 | 4324239 | a | 0 | + | | chr18 | 8915283 | 8922757 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4cyl60c5/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 4323803 4324239 + 1 chr1 5924745 5929982 + 1 chr1 7347229 7349479 + 1 chr18 8915283 8922757 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 4323803 4324239 + 1 1 chr1 5924745 5929982 + 1 2 chr1 7347229 7349479 + 1 3 chr18 8915283 8922757 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 202498 | 202755 | a | 0 | + | | chr1 | 65818 | 66324 | a | 0 | - | | chr1 | 6844445 | 6854231 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp8f4aepwd/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65818 66324 - 1 chr1 202498 202755 + 1 chr1 6844445 6854231 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 65818 66324 - 1 1 chr1 202498 202755 + 1 2 chr1 6844445 6854231 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6867204 | 6869619 | a | 0 | + | | chr1 | 4456546 | 4465657 | a | 0 | - | | chr1 | 1877491 | 1883897 | a | 0 | - | | chr15 | 6109712 | 6118229 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0ydrgqs8/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1877491 1883897 - 1 chr1 4456546 4465657 - 1 chr1 6867204 6869619 + 1 chr15 6109712 6118229 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1877491 1883897 - 1 1 chr1 4456546 4465657 - 1 2 chr1 6867204 6869619 + 1 3 chr15 6109712 6118229 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9259536 | 9264487 | a | 0 | - | | chr19 | 5899008 | 5901837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp0ja3oe2b/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9259536 9264487 - 1 chr19 5899008 5901837 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9259536 9264487 - 1 1 chr19 5899008 5901837 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 9259536 | 9264487 | a | 0 | - | | chr19 | 5899008 | 5901837 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpe1qebksv/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 9259536 9264487 - 1 chr19 5899008 5901837 - 1 bedtools_df Chromosome Start End Strand Count 0 chr1 9259536 9264487 - 1 1 chr19 5899008 5901837 - 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr19 | 1794 | 11793 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmprpssiupl/f1.bed) resultresultresultresultresultresultresultresultresultresult chr19 1794 11793 + 1 bedtools_df Chromosome Start End Strand Count 0 chr19 1794 11793 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6941308 | 6942901 | a | 0 | + | | chr1 | 65305 | 72731 | a | 0 | + | | chr22 | 6025964 | 6033374 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpturcxg9c/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 65305 72731 + 1 chr1 6941308 6942901 + 1 chr22 6025964 6033374 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 65305 72731 + 1 1 chr1 6941308 6942901 + 1 2 chr22 6025964 6033374 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp4k44y3p_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpfr2_svug/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpsti0mlgn/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmppbkfte4l/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmp9k9xx9ky/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmphik759p2/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -s -i <(sort -k1,1 -k2,2n /tmp/tmpg_r5v016/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 bedtools_df Chromosome Start End Strand Count 0 chr1 1 2 + 1 ______________________________ test_merge[False] _______________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:31: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:75: in test_merge result = gr.merge(strand=strand, count=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:381: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_merge( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strand=False, E ) sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp6ihsbx3d/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 2576654 | 2578864 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpdyycb533/f1.bed) resultresultresultresultresultresultresultresultresultresult chr2 2576654 2578864 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr2 2576654 2578864 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3332478 | 3332670 | a | 0 | + | | chr1 | 1894553 | 1900020 | a | 0 | + | | chr1 | 8853754 | 8862003 | a | 0 | - | | chr1 | 10000000 | 10009026 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr8 | 3051398 | 3058477 | a | 0 | - | | chrM | 6021873 | 6028653 | a | 0 | + | | chrM | 5209885 | 5215437 | a | 0 | + | | chrX | 7777273 | 7786876 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 6 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpg6ku1hs4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1894553 1900020 + 1 chr1 3332478 3332670 + 1 chr1 5209885 5214946 - 1 chr1 8853754 8862003 - 1 chr1 10000000 10009026 - 1 chr2 8699854 8703183 - 1 chr6 8699909 8706150 - 1 chr8 3051398 3058477 - 1 chrM 5209885 5215437 + 1 chrM 6021873 6028653 + 1 chrX 7777273 7786876 - 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1894553 1900020 1 1 chr1 3332478 3332670 1 2 chr1 5209885 5214946 1 3 chr1 8853754 8862003 1 4 chr1 10000000 10009026 1 5 chr2 8699854 8703183 1 6 chr6 8699909 8706150 1 7 chr8 3051398 3058477 1 8 chrM 5209885 5215437 1 9 chrM 6021873 6028653 1 10 chrX 7777273 7786876 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2985826 | 2990807 | a | 0 | + | | chr1 | 904246 | 911797 | a | 0 | - | | chr1 | 8519760 | 8524991 | a | 0 | - | | chr1 | 7674085 | 7675447 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr16 | 2085589 | 2094114 | a | 0 | - | | chr17 | 102890 | 107436 | a | 0 | + | | chr17 | 3634561 | 3636945 | a | 0 | + | | chr21 | 6895997 | 6904522 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 7 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp9z2ge5af/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 904246 911797 - 1 chr1 2985826 2990807 + 1 chr1 7674085 7675447 - 1 chr1 8519760 8524991 - 1 chr15 4366550 4372645 - 1 chr16 2085589 2094114 - 1 chr17 102890 107436 + 1 chr17 3634561 3636945 + 1 chr2 2929013 2930049 + 1 chr21 6895997 6904522 + 1 chr9 3935100 3936105 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 904246 911797 1 1 chr1 2985826 2990807 1 2 chr1 7674085 7675447 1 3 chr1 8519760 8524991 1 4 chr15 4366550 4372645 1 5 chr16 2085589 2094114 1 6 chr17 102890 107436 1 7 chr17 3634561 3636945 1 8 chr2 2929013 2930049 1 9 chr21 6895997 6904522 1 10 chr9 3935100 3936105 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5638606 | 5641819 | a | 0 | - | | chr10 | 3747054 | 3754279 | a | 0 | + | | chr10 | 2784396 | 2787873 | a | 0 | - | | chr11 | 2712749 | 2714705 | a | 0 | - | | chr22 | 3442480 | 3448605 | a | 0 | - | | chr22 | 3639006 | 3639515 | a | 0 | - | | chrY | 4788375 | 4789569 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpsyg8bmn_/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5638606 5641819 - 1 chr10 2784396 2787873 - 1 chr10 3747054 3754279 + 1 chr11 2712749 2714705 - 1 chr22 3442480 3448605 - 1 chr22 3639006 3639515 - 1 chrY 4788375 4789569 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5638606 5641819 1 1 chr10 2784396 2787873 1 2 chr10 3747054 3754279 1 3 chr11 2712749 2714705 1 4 chr22 3442480 3448605 1 5 chr22 3639006 3639515 1 6 chrY 4788375 4789569 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2123715 | 2128635 | a | 0 | + | | chr1 | 4084554 | 4093081 | a | 0 | + | | chr1 | 2655627 | 2657093 | a | 0 | + | | chr1 | 883284 | 884058 | a | 0 | - | | chr2 | 9266985 | 9270536 | a | 0 | + | | chr4 | 9321624 | 9325158 | a | 0 | + | | chr14 | 3940262 | 3947259 | a | 0 | + | | chr14 | 6004200 | 6012339 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp76elbsah/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 883284 884058 - 1 chr1 2123715 2128635 + 1 chr1 2655627 2657093 + 1 chr1 4084554 4093081 + 1 chr14 3940262 3947259 + 1 chr14 6004200 6012339 + 1 chr2 9266985 9270536 + 1 chr4 9321624 9325158 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 883284 884058 1 1 chr1 2123715 2128635 1 2 chr1 2655627 2657093 1 3 chr1 4084554 4093081 1 4 chr14 3940262 3947259 1 5 chr14 6004200 6012339 1 6 chr2 9266985 9270536 1 7 chr4 9321624 9325158 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 7701404 | 7709945 | a | 0 | - | | chr2 | 4881953 | 4888207 | a | 0 | + | | chr3 | 4584320 | 4588793 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpqo8ynb43/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 7701404 7709945 - 1 chr2 4881953 4888207 + 1 chr3 4584320 4588793 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 7701404 7709945 1 1 chr2 4881953 4888207 1 2 chr3 4584320 4588793 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5947879 | 5952843 | a | 0 | + | | chr1 | 5197359 | 5202842 | a | 0 | + | | chr1 | 10000000 | 10008136 | a | 0 | - | | chr2 | 5397264 | 5401353 | a | 0 | + | | chr18 | 6440877 | 6442440 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp39wup51o/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 5197359 5202842 + 1 chr1 5947879 5952843 + 1 chr1 10000000 10008136 - 1 chr18 6440877 6442440 - 1 chr2 5397264 5401353 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 5197359 5202842 1 1 chr1 5947879 5952843 1 2 chr1 10000000 10008136 1 3 chr18 6440877 6442440 1 4 chr2 5397264 5401353 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 394755 | 396720 | a | 0 | + | | chr1 | 5397264 | 5399229 | a | 0 | + | | chr1 | 66561 | 76561 | a | 0 | - | | chr1 | 721156 | 723121 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpk7qdcufa/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 66561 76561 - 1 chr1 394755 396720 + 1 chr1 721156 723121 - 1 chr1 5397264 5399229 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 66561 76561 1 1 chr1 394755 396720 1 2 chr1 721156 723121 1 3 chr1 5397264 5399229 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8194492 | 8198175 | a | 0 | - | | chr2 | 627746 | 635365 | a | 0 | + | | chr3 | 8067755 | 8068323 | a | 0 | + | | chr12 | 5038850 | 5040289 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp2j2es0sb/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 8194492 8198175 - 1 chr12 5038850 5040289 + 1 chr2 627746 635365 + 1 chr3 8067755 8068323 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 8194492 8198175 1 1 chr12 5038850 5040289 1 2 chr2 627746 635365 1 3 chr3 8067755 8068323 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpx1zhp2ry/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpwp4bsbxw/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpib9dijc4/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpj482szzg/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpev0t05_q/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmpfv_1aeft/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools merge -o first,count -c 6,1 -i <(sort -k1,1 -k2,2n /tmp/tmp7of_g5g7/f1.bed) resultresultresultresultresultresultresultresultresultresult chr1 1 2 + 1 if not if not if not if not if not if not if not if not if not if not bedtools_df Chromosome Start End Count 0 chr1 1 2 1 _____________________________ test_cluster[False] ______________________________ [gw0] linux -- Python 3.11.2 /usr/bin/python3.11 strand = False @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:133: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strand=False, E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpl4yenp8_/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3333023 | 3339938 | a | 0 | + | | chr1 | 3333023 | 3341309 | a | 0 | + | | chr1 | 7339348 | 7345979 | a | 0 | - | | chr1 | 7541276 | 7547907 | a | 0 | - | | chr1 | 3333023 | 3339654 | a | 0 | - | | chr1 | 3333023 | 3341804 | a | 0 | - | | chr1 | 9932901 | 9942291 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpryuzx7hd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3333023 3339654 a 0 - 1 1 chr1 3333023 3339938 a 0 + 1 2 chr1 3333023 3341309 a 0 + 1 3 chr1 3333023 3341804 a 0 - 1 4 chr1 7339348 7345979 a 0 - 2 5 chr1 7541276 7547907 a 0 - 3 6 chr1 9932901 9942291 a 0 - 4 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3333023 | 3339938 | a | 0 | + | | chr1 | 3333023 | 3341309 | a | 0 | + | | chr1 | 7339348 | 7345979 | a | 0 | - | | chr1 | 7541276 | 7547907 | a | 0 | - | | chr1 | 3333023 | 3339654 | a | 0 | - | | chr1 | 3333023 | 3341804 | a | 0 | - | | chr1 | 9932901 | 9942291 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr16 | 1939946 | 1947345 | a | 0 | - | | chr18 | 3778076 | 3787014 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_ohshplu/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr16 1939946 1947345 a 0 - 1 1 chr18 3778076 3787014 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr16 | 1939946 | 1947345 | a | 0 | - | | chr18 | 3778076 | 3787014 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3666814 | 3669812 | a | 0 | + | | chr16 | 9856845 | 9862454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp07n6fy0m/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3666814 3669812 a 0 + 1 1 chr16 9856845 9862454 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3666814 | 3669812 | a | 0 | + | | chr16 | 9856845 | 9862454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3666814 | 3669812 | a | 0 | + | | chr16 | 9856845 | 9862454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp29nttakl/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3666814 3669812 a 0 + 1 1 chr16 9856845 9862454 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3666814 | 3669812 | a | 0 | + | | chr16 | 9856845 | 9862454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3666814 | 3669812 | a | 0 | + | | chr16 | 9856845 | 9862454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpe4auj5r1/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3666814 3669812 a 0 + 1 1 chr16 9856845 9862454 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3666814 | 3669812 | a | 0 | + | | chr16 | 9856845 | 9862454 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2728360 | 2737486 | a | 0 | + | | chr1 | 4689947 | 4690413 | a | 0 | - | | chr1 | 546105 | 553097 | a | 0 | - | | chr3 | 2440615 | 2447607 | a | 0 | + | | chr8 | 1528727 | 1536646 | a | 0 | + | | chr11 | 7816965 | 7824677 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpg_ndzt7p/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 546105 553097 a 0 - 1 1 chr1 2728360 2737486 a 0 + 2 2 chr1 4689947 4690413 a 0 - 3 3 chr11 7816965 7824677 a 0 - 4 4 chr3 2440615 2447607 a 0 + 5 5 chr8 1528727 1536646 a 0 + 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2728360 | 2737486 | a | 0 | + | | chr1 | 4689947 | 4690413 | a | 0 | - | | chr1 | 546105 | 553097 | a | 0 | - | | chr3 | 2440615 | 2447607 | a | 0 | + | | chr8 | 1528727 | 1536646 | a | 0 | + | | chr11 | 7816965 | 7824677 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 6 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2094365 | 2103311 | a | 0 | + | | chrY | 5626696 | 5626697 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp70lo2v4l/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2094365 2103311 a 0 + 1 1 chrY 5626696 5626697 a 0 + 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2094365 | 2103311 | a | 0 | + | | chrY | 5626696 | 5626697 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5897 | 8715 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpiqrjlptg/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5897 8715 a 0 - 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5897 | 8715 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3951725 | 3960218 | a | 0 | + | | chr1 | 1232980 | 1242262 | a | 0 | - | | chr1 | 1232980 | 1237738 | a | 0 | - | | chr1 | 6663967 | 6672872 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1232980 | 1237738 | a | 0 | - | | chr1 | 6663967 | 6672872 | a | 0 | - | | chr1 | 1232980 | 1240648 | a | 0 | - | | chr1 | 1232980 | 1240904 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpuk4do5aw/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1232980 1237738 a 0 - 1 1 chr1 1232980 1240648 a 0 - 1 2 chr1 1232980 1240904 a 0 - 1 3 chr1 1232980 1242262 a 0 - 1 4 chr1 3951725 3960218 a 0 + 2 5 chr1 6663967 6672872 a 0 - 3 6 chr12 2 432 a 0 + 4 7 chr8 7292031 7293863 a 0 + 5 8 chrX 793010 793011 a 0 - 6 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3951725 | 3960218 | a | 0 | + | | chr1 | 1232980 | 1242262 | a | 0 | - | | chr1 | 1232980 | 1237738 | a | 0 | - | | chr1 | 6663967 | 6672872 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 1232980 | 1237738 | a | 0 | - | | chr1 | 6663967 | 6672872 | a | 0 | - | | chr1 | 1232980 | 1240648 | a | 0 | - | | chr1 | 1232980 | 1240904 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 9 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmply9vye86/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpp1gyny_z/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpfarb4sei/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpay9sv0gx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp_shv950n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmp714ltyxx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -i <(sort -k1,1 -k2,2n /tmp/tmpmtme0qvj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. _____________________________ test_introns_single ______________________________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 def test_introns_single(): "Assert that our fast method of computing introns is the same as the slow, correct one in compute_introns_single" gr = pr.data.gencode_gtf()[["gene_id", "Feature"]] exons = gr[gr.Feature == "exon"].merge(by="gene_id") exons.Feature = "exon" exons = exons.df df = pd.concat([gr[gr.Feature == "gene"].df, exons], sort=False) print(df) for gid, gdf in df.groupby("gene_id"): print("-------" * 20) print(gid) print(gdf) print("gdf", len(gdf)) expected = compute_introns_single(gdf, by="gene") print("expected", len(expected)) > actual = pr.PyRanges(gdf).features.introns().df tests/test_genomicfeatures.py:174: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/genomicfeatures.py:254: in introns result = pyrange_apply(_introns2, by_gr, exons, **kwargs) pyranges/multithreaded.py:292: in pyrange_apply result = call_f(function, nparams, df, odf, kwargs) pyranges/multithreaded.py:22: in call_f return f.remote(df, odf, **kwargs) pyranges/genomicfeatures.py:567: in _introns2 starts, ends, ids = find_introns(genes.Start.values, genes.End.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'const long' but got 'long long' sorted_nearest/src/introns.pyx:12: ValueError ----------------------------- Captured stdout call ----------------------------- Chromosome gene_id Start End Strand Feature 0 chr1 ENSG00000223972.5 11868 14409 + gene 1 chr1 ENSG00000243485.5 29553 31109 + gene 2 chr1 ENSG00000284332.1 30365 30503 + gene 3 chr1 ENSG00000268020.3 52472 53312 + gene 4 chr1 ENSG00000240361.2 57597 64116 + gene .. ... ... ... ... ... ... 587 chr1 ENSG00000283040.1 876754 877234 - exon 588 chr1 ENSG00000283712.1 1312501 1312566 - exon 589 chr1 ENSG00000284372.1 1339649 1339708 - exon 590 chr1 ENSG00000284662.1 685678 686673 - exon 591 chr1 ENSG00000284733.1 450702 451697 - exon [711 rows x 6 columns] -------------------------------------------------------------------------------------------------------------------------------------------- ENSG00000078808.16 Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene 284 chr1 ENSG00000078808.16 1216907 1217804 - exon 285 chr1 ENSG00000078808.16 1218457 1221351 - exon 286 chr1 ENSG00000078808.16 1223243 1223357 - exon 287 chr1 ENSG00000078808.16 1223831 1223968 - exon 288 chr1 ENSG00000078808.16 1227271 1227319 - exon 289 chr1 ENSG00000078808.16 1228467 1228946 - exon 290 chr1 ENSG00000078808.16 1231891 1232031 - exon gdf 8 g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g g Chromosome gene_id Start End Strand Feature 101 chr1 ENSG00000078808.16 1216907 1232031 - gene x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x Chromosome Start End gene_id Strand 0 chr1 1216907 1217804 ENSG00000078808.16 - 1 chr1 1218457 1221351 ENSG00000078808.16 - 2 chr1 1223243 1223357 ENSG00000078808.16 - 3 chr1 1223831 1223968 ENSG00000078808.16 - 4 chr1 1227271 1227319 ENSG00000078808.16 - 5 chr1 1228467 1228946 ENSG00000078808.16 - 6 chr1 1231891 1232031 ENSG00000078808.16 - expected 6 __________ test_three_in_a_row[strandedness_chain434-method_chain434] __________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strandedness_chain = ('opposite', None), method_chain = ('join', 'set_union') @pytest.mark.bedtools > @pytest.mark.parametrize("strandedness_chain,method_chain", product(strandedness_chain, method_chain)) tests/test_do_not_error.py:40: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_do_not_error.py:82: in test_three_in_a_row gr3 = m2(gr3, strandedness=s2) pyranges/pyranges.py:3784: in set_union gr = gr.merge(strand=strand) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_three_in_a_row( E gr=Empty PyRanges, E gr2=Empty PyRanges, E gr3=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strandedness_chain=('opposite', None), E method_chain=('join', 'set_union'), E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2BkgAFGFAoMAABaAAQ=') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') Empty PyRanges ('join', 'set_union') ______________________________ test_cluster[True] ______________________________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 strand = True @pytest.mark.bedtools > @pytest.mark.parametrize("strand", [True, False]) tests/test_unary.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:133: in test_cluster result = gr.cluster(strand=strand) pyranges/pyranges.py:1070: in cluster df = pyrange_apply_single(_cluster, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/cluster.py:14: in _cluster ids = annotate_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_cluster( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E strand=True, E ) sorted_nearest/src/annotate_clusters.pyx:15: Exception ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmppp4vgr3y/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3804931 | 3805213 | a | 0 | + | | chr13 | 7835653 | 7840966 | a | 0 | - | | chr22 | 7835653 | 7843986 | a | 0 | + | | chrM | 2493371 | 2499305 | a | 0 | + | | chrX | 7835653 | 7835935 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpuo7vhc9n/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3804931 3805213 a 0 + 1 1 chr13 7835653 7840966 a 0 - 2 2 chr22 7835653 7843986 a 0 + 3 3 chrM 2493371 2499305 a 0 + 4 4 chrX 7835653 7835935 a 0 - 5 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3804931 | 3805213 | a | 0 | + | | chr13 | 7835653 | 7840966 | a | 0 | - | | chr22 | 7835653 | 7843986 | a | 0 | + | | chrM | 2493371 | 2499305 | a | 0 | + | | chrX | 7835653 | 7835935 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 5 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3159016 | 3167039 | a | 0 | - | | chr1 | 4030078 | 4034845 | a | 0 | - | | chr19 | 2702449 | 2704990 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpy8rnl2sx/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 3159016 3167039 a 0 - 1 1 chr1 4030078 4034845 a 0 - 2 2 chr19 2702449 2704990 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3159016 | 3167039 | a | 0 | - | | chr1 | 4030078 | 4034845 | a | 0 | - | | chr19 | 2702449 | 2704990 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6993597 | 6999679 | a | 0 | - | | chr1 | 6935499 | 6935795 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmmhaa213/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 6935499 6935795 a 0 - 1 1 chr1 6993597 6999679 a 0 - 2 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 6993597 | 6999679 | a | 0 | - | | chr1 | 6935499 | 6935795 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2071283 | 2079193 | a | 0 | + | | chr1 | 6464776 | 6473089 | a | 0 | + | | chr1 | 8925593 | 8935593 | a | 0 | - | | chr1 | 2408314 | 2412966 | a | 0 | - | | chr1 | 5466639 | 5471143 | a | 0 | - | | chr1 | 2192155 | 2196807 | a | 0 | - | | chrY | 6772969 | 6777621 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmps76f8b67/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 2071283 2079193 a 0 + 1 1 chr1 6464776 6473089 a 0 + 2 2 chr1 2192155 2196807 a 0 - 3 3 chr1 2408314 2412966 a 0 - 4 4 chr1 5466639 5471143 a 0 - 5 5 chr1 8925593 8935593 a 0 - 6 6 chrY 6772969 6777621 a 0 + 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 2071283 | 2079193 | a | 0 | + | | chr1 | 6464776 | 6473089 | a | 0 | + | | chr1 | 8925593 | 8935593 | a | 0 | - | | chr1 | 2408314 | 2412966 | a | 0 | - | | chr1 | 5466639 | 5471143 | a | 0 | - | | chr1 | 2192155 | 2196807 | a | 0 | - | | chrY | 6772969 | 6777621 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 7 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1941104 | 1951104 | a | 0 | + | | chr1 | 2306541 | 2312180 | a | 0 | + | | chr1 | 2190903 | 2194461 | a | 0 | + | | chr1 | 5196545 | 5206545 | a | 0 | - | | chr1 | 4832419 | 4836121 | a | 0 | - | | chr1 | 6861798 | 6869131 | a | 0 | - | | chr1 | 8310889 | 8316528 | a | 0 | - | | chr17 | 7702035 | 7702456 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpbg3hru2c/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1941104 1951104 a 0 + 1 1 chr1 2190903 2194461 a 0 + 2 2 chr1 2306541 2312180 a 0 + 3 3 chr1 4832419 4836121 a 0 - 4 4 chr1 5196545 5206545 a 0 - 5 5 chr1 6861798 6869131 a 0 - 6 6 chr1 8310889 8316528 a 0 - 7 7 chr17 7702035 7702456 a 0 + 8 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1941104 | 1951104 | a | 0 | + | | chr1 | 2306541 | 2312180 | a | 0 | + | | chr1 | 2190903 | 2194461 | a | 0 | + | | chr1 | 5196545 | 5206545 | a | 0 | - | | chr1 | 4832419 | 4836121 | a | 0 | - | | chr1 | 6861798 | 6869131 | a | 0 | - | | chr1 | 8310889 | 8316528 | a | 0 | - | | chr17 | 7702035 | 7702456 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 8 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4607328 | 4608874 | a | 0 | - | | chr1 | 452478 | 460483 | a | 0 | - | | chr14 | 2298466 | 2300129 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpvlzkddws/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 452478 460483 a 0 - 1 1 chr1 4607328 4608874 a 0 - 2 2 chr14 2298466 2300129 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4607328 | 4608874 | a | 0 | - | | chr1 | 452478 | 460483 | a | 0 | - | | chr14 | 2298466 | 2300129 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4607328 | 4608874 | a | 0 | - | | chr1 | 452478 | 460483 | a | 0 | - | | chr14 | 2298466 | 2300129 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmplf6gu6tt/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 452478 460483 a 0 - 1 1 chr1 4607328 4608874 a 0 - 2 2 chr14 2298466 2300129 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 4607328 | 4608874 | a | 0 | - | | chr1 | 452478 | 460483 | a | 0 | - | | chr14 | 2298466 | 2300129 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 66104 | 69690 | a | 0 | + | | chr1 | 66104 | 69690 | a | 0 | - | | chr2 | 66104 | 69690 | a | 0 | + | | chr4 | 66305 | 69891 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 66104 | 69690 | a | 0 | + | | chr4 | 66104 | 69690 | a | 0 | + | | chr4 | 66104 | 69690 | a | 0 | - | | chr4 | 66104 | 69690 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpnz1gozb6/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 66104 69690 a 0 + 1 1 chr1 66104 69690 a 0 - 2 2 chr12 66308 69894 a 0 + 3 3 chr2 66104 69690 a 0 + 4 4 chr4 66104 69690 a 0 + 5 5 chr4 66104 69690 a 0 + 5 6 chr4 66104 69690 a 0 + 5 7 chr4 66305 69891 a 0 + 5 8 chr4 93247 100929 a 0 + 6 9 chr4 66104 69690 a 0 - 7 10 chr4 66104 69690 a 0 - 7 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 66104 | 69690 | a | 0 | + | | chr1 | 66104 | 69690 | a | 0 | - | | chr2 | 66104 | 69690 | a | 0 | + | | chr4 | 66305 | 69891 | a | 0 | + | | ... | ... | ... | ... | ... | ... | | chr4 | 66104 | 69690 | a | 0 | + | | chr4 | 66104 | 69690 | a | 0 | + | | chr4 | 66104 | 69690 | a | 0 | - | | chr4 | 66104 | 69690 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 11 rows and 6 columns from 4 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5168348 | 5168350 | a | 0 | + | | chr1 | 5168348 | 5175441 | a | 0 | + | | chr1 | 5168348 | 5177593 | a | 0 | - | | chr1 | 5168348 | 5176829 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5168348 | 5169455 | a | 0 | - | | chr1 | 5168348 | 5174193 | a | 0 | - | | chr1 | 5168348 | 5172196 | a | 0 | - | | chr1 | 5168348 | 5176832 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpzad3ean2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 5168348 5168350 a 0 + 1 1 chr1 5168348 5175441 a 0 + 1 2 chr1 5168348 5169455 a 0 - 2 3 chr1 5168348 5169692 a 0 - 2 4 chr1 5168348 5172196 a 0 - 2 5 chr1 5168348 5174193 a 0 - 2 6 chr1 5168348 5176829 a 0 - 2 7 chr1 5168348 5176832 a 0 - 2 8 chr1 5168348 5177593 a 0 - 2 9 chr11 5168348 5170360 a 0 - 3 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 5168348 | 5168350 | a | 0 | + | | chr1 | 5168348 | 5175441 | a | 0 | + | | chr1 | 5168348 | 5177593 | a | 0 | - | | chr1 | 5168348 | 5176829 | a | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 5168348 | 5169455 | a | 0 | - | | chr1 | 5168348 | 5174193 | a | 0 | - | | chr1 | 5168348 | 5172196 | a | 0 | - | | chr1 | 5168348 | 5176832 | a | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpcu_i18c2/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmncu4w7g/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpk6orzl5y/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpi8abfp6o/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpf5ynegfd/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpxn2c1ohj/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. bedtools cluster -s -i <(sort -k1,1 -k2,2n /tmp/tmpmim1e72y/f1.bed) bedtools_df Chromosome Start End Name Score Strand Cluster 0 chr1 1 2 a 0 + 1 gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int64) | (int64) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. _________________________________ test_summary _________________________________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 @pytest.mark.bedtools > @settings( max_examples=max_examples, deadline=deadline, print_blob=True, suppress_health_check=HealthCheck.all()) tests/test_unary.py:313: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:324: in test_summary gr.summary() pyranges/pyranges.py:4475: in summary return _summary(self, to_stdout, return_df) pyranges/methods/summary.py:16: in _summary c = self.merge(strand=True) pyranges/pyranges.py:2835: in merge df = pyrange_apply_single(_merge, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/merge.py:16: in _merge starts, ends, number = find_clusters(cdf.Start.values, cdf.End.values, slack) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_summary( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBAAAADIAAw==') as a decorator on your test case sorted_nearest/src/clusters.pyx:16: Exception ----------------------------- Captured stdout call ----------------------------- {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr3', 'chr4', 'chr6', 'chr11', 'chr15'], 'Start': [9679741, 9914512, 9314315, 8484192, 9442071, 561150, 5584741, 5674760, 4457374, 8373763], 'End': [9687254, 9923026, 9318572, 8488192, 9450585, 562840, 5593255, 5683274, 4465888, 8382277], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '-', '-', '-', '-', '+', '+', '-', '-']} {'Chromosome': ['chr4', 'chr7', 'chr15', 'chr15', 'chr15', 'chr16'], 'Start': [5960686, 5312594, 6514805, 1678485, 1542747, 9985251], 'End': [5965104, 5321612, 6523626, 1687044, 1551473, 9990889], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['-', '-', '+', '-', '-', '+']} {'Chromosome': ['chr1', 'chrX'], 'Start': [2813723, 5446079], 'End': [2820332, 5446081], 'Name': ['a', 'a'], 'Score': [0, 0], 'Strand': ['+', '+']} {'Chromosome': ['chr1'], 'Start': [65793], 'End': [65910], 'Name': ['a'], 'Score': [0], 'Strand': ['-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr4'], 'Start': [3084796, 205096, 1487914, 342461, 4778306, 7981736], 'End': [3084798, 205413, 1492927, 349590, 4788269, 7988282], 'Name': ['a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '-', '-', '-']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr4'], 'Start': [424395, 66127, 3473669, 2172688, 4263426], 'End': [424653, 66385, 3473927, 2172952, 4263684], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr4'], 'Start': [424395, 66127, 3473669, 2172688, 4263426], 'End': [424653, 66385, 3473927, 2172952, 4263684], 'Name': ['a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '+']} {'Chromosome': ['chr1', 'chr1', 'chr6'], 'Start': [387621, 3088458, 1879182], 'End': [394150, 3093821, 1879990], 'Name': ['a', 'a', 'a'], 'Score': [0, 0, 0], 'Strand': ['+', '-', '+']} {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr5', 'chr5', 'chr6', 'chr11', 'chr19'], 'Start': [1052320, 4099442, 9824149, 3150464, 8498969, 3997041, 1681391, 3402310, 1791173, 6441535], 'End': [1055295, 4103457, 9824499, 3154431, 8501846, 3998439, 1681811, 3410257, 1797041, 6449766], 'Name': ['a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a'], 'Score': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'Strand': ['+', '+', '+', '+', '-', '-', '-', '+', '-', '+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} {'Chromosome': ['chr1'], 'Start': [1], 'End': [2], 'Name': ['a'], 'Score': [0], 'Strand': ['+']} _________________________________ test_windows _________________________________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 def test_windows(): f1 = pr.data.f1() print(f1) > result = f1.tile(2) tests/windows/test_windows.py:25: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:25: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:49: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. ________________________________ test_windows2 _________________________________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 def test_windows2(): c = """Chromosome Start End Count 0 chr1 10200 10400 7 1 chr1 10400 10600 7 2 chr1 51400 51600 1 3 chr1 51600 51800 3 4 chr1 51800 52000 3""" df = pd.read_csv(StringIO(c), sep=r"\s+", nrows=5) # df.End -= 1 gr = pr.PyRanges(df) print(gr) > result = gr.tile(200) tests/windows/test_windows.py:48: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pyranges/pyranges.py:4649: in tile df = pyrange_apply_single(_tiles, self, **kwargs) pyranges/multithreaded.py:360: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:40: in _tiles idxs, starts, ends = maketiles(df.index.values, df.Start.values, sorted_nearest/src/tiles.pyx:25: in sorted_nearest.src.tiles.maketiles ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E ValueError: Buffer dtype mismatch, expected 'long' but got 'long long' sorted_nearest/src/tiles.pyx:49: ValueError ----------------------------- Captured stdout call ----------------------------- +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | Count | | (category) | (int32) | (int32) | (int64) | |--------------+-----------+-----------+-----------| | chr1 | 10200 | 10400 | 7 | | chr1 | 10400 | 10600 | 7 | | chr1 | 51400 | 51600 | 1 | | chr1 | 51600 | 51800 | 3 | | chr1 | 51800 | 52000 | 3 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 5 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome. _________________________________ test_windows _________________________________ [gw3] linux -- Python 3.11.2 /usr/bin/python3.11 @pytest.mark.bedtools > @settings( max_examples=max_examples, print_blob=True, deadline=deadline, suppress_health_check=HealthCheck.all()) tests/test_unary.py:231: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_unary.py:261: in test_windows result = gr.window(10)["Chromosome Start End".split()].unstrand() pyranges/pyranges.py:5485: in window df = pyrange_apply_single(_windows, self, **kwargs) pyranges/multithreaded.py:347: in pyrange_apply_single result = call_f_single(function, nparams, df, **kwargs) pyranges/multithreaded.py:30: in call_f_single return f.remote(df, **kwargs) pyranges/methods/windows.py:11: in _windows idxs, starts, ends = makewindows(df.index.values, df.Start.values, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E Exception: Starts/Ends not int64 or int32: int64 E Falsifying example: test_windows( E gr=+--------------+-----------+-----------+------------+-----------+--------------+ E | Chromosome | Start | End | Name | Score | Strand | E | (category) | (int64) | (int64) | (object) | (int64) | (category) | E |--------------+-----------+-----------+------------+-----------+--------------| E | chr1 | 1 | 2 | a | 0 | + | E +--------------+-----------+-----------+------------+-----------+--------------+ E Stranded PyRanges object has 1 rows and 6 columns from 1 chromosomes. E For printing, the PyRanges was sorted on Chromosome and Strand., E ) E E You can reproduce this example by temporarily adding @reproduce_failure('6.67.1', b'AXicY2QAA0YGBAAAADIAAw==') as a decorator on your test case sorted_nearest/src/windows.pyx:22: Exception ----------------------------- Captured stdout call ----------------------------- bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp9oh3oycy/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpv_2sg3l0/f1.bed) bedtools_df Chromosome Start End 0 chr1 8222196 8222206 1 chr1 8222206 8222216 2 chr1 8222216 8222226 3 chr1 8222226 8222236 4 chr1 8222236 8222246 .. ... ... ... 503 chr20 1688904 1688914 504 chr20 1688914 1688924 505 chr20 1688924 1688934 506 chr20 1688934 1688944 507 chr20 1688944 1688948 [508 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpymvog3_2/f1.bed) bedtools_df Chromosome Start End 0 chr20 1282 1292 1 chr20 1292 1302 2 chr20 1302 1312 3 chr20 1312 1322 4 chr20 1322 1332 5 chr20 1332 1342 6 chr20 1342 1352 7 chr20 1352 1362 8 chr20 1362 1372 9 chr20 1372 1382 10 chr20 1382 1392 11 chr20 1392 1402 12 chr20 1402 1412 13 chr20 1412 1422 14 chr20 1422 1432 15 chr20 1432 1442 16 chr20 1442 1452 17 chr20 1452 1462 18 chr20 1462 1472 19 chr20 1472 1482 20 chr20 1482 1492 21 chr20 1492 1502 22 chr20 1502 1512 23 chr20 1512 1522 24 chr20 1522 1532 25 chr20 1532 1542 26 chr20 1542 1552 27 chr20 1552 1562 28 chr20 1562 1572 29 chr20 1572 1582 30 chr20 1582 1592 31 chr20 1592 1602 32 chr20 1602 1612 33 chr20 1612 1622 34 chr20 1622 1632 35 chr20 1632 1642 36 chr20 1642 1652 37 chr20 1652 1662 38 chr20 1662 1672 39 chr20 1672 1682 40 chr20 1682 1692 41 chr20 1692 1702 42 chr20 1702 1712 43 chr20 1712 1722 44 chr20 1722 1732 45 chr20 1732 1742 46 chr20 1742 1752 47 chr20 1752 1762 48 chr20 1762 1772 49 chr20 1772 1782 50 chr20 1782 1786 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpy54d2ocz/f1.bed) bedtools_df Chromosome Start End 0 chr1 1905098 1905108 1 chr1 1905108 1905118 2 chr1 1905118 1905128 3 chr1 1905128 1905138 4 chr1 1905138 1905148 ... ... ... ... 2267 chr13 2503547 2503557 2268 chr13 2503557 2503567 2269 chr13 2503567 2503577 2270 chr13 2503577 2503587 2271 chr13 2503587 2503595 [2272 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpr46q1awy/f1.bed) bedtools_df Chromosome Start End 0 chr1 601231 601241 1 chr1 601241 601251 2 chr1 601251 601261 3 chr1 601261 601271 4 chr1 601271 601281 ... ... ... ... 1950 chr1 10009029 10009039 1951 chr1 10009039 10009049 1952 chr1 10009049 10009059 1953 chr1 10009059 10009069 1954 chr1 10009069 10009076 [1955 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmptou9r0i9/f1.bed) bedtools_df Chromosome Start End 0 chr1 7848263 7848273 1 chr1 7848273 7848283 2 chr1 7848283 7848293 3 chr1 7848293 7848303 4 chr1 7848303 7848313 ... ... ... ... 1241 chr19 7850183 7850193 1242 chr19 7850193 7850203 1243 chr19 7850203 7850213 1244 chr19 7850213 7850223 1245 chr19 7850223 7850233 [1246 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpji99k_wc/f1.bed) bedtools_df Chromosome Start End 0 chr1 2059929 2059939 1 chr1 2059939 2059949 2 chr1 2059949 2059959 3 chr1 2059959 2059969 4 chr1 2059969 2059979 5 chr1 2059979 2059989 6 chr1 2059989 2059999 7 chr1 2059999 2060009 8 chr1 2060009 2060019 9 chr1 2060019 2060029 10 chr1 2060029 2060039 11 chr1 2060039 2060049 12 chr1 2060049 2060059 13 chr1 2060059 2060069 14 chr1 2060069 2060079 15 chr1 2060079 2060089 16 chr1 2060089 2060099 17 chr1 2060099 2060109 18 chr1 2060109 2060119 19 chr1 2060119 2060129 20 chr1 2060129 2060139 21 chr1 2060139 2060149 22 chr1 2060149 2060159 23 chr1 2060159 2060169 24 chr1 2060169 2060179 25 chr1 2060179 2060187 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp_k8qbsdx/f1.bed) bedtools_df Chromosome Start End 0 chr1 2059929 2059939 1 chr1 2059939 2059949 2 chr1 2059949 2059959 3 chr1 2059959 2059969 4 chr1 2059969 2059979 5 chr1 2059979 2059989 6 chr1 2059989 2059999 7 chr1 2059999 2060009 8 chr1 2060009 2060019 9 chr1 2060019 2060029 10 chr1 2060029 2060039 11 chr1 2060039 2060049 12 chr1 2060049 2060059 13 chr1 2060059 2060069 14 chr1 2060069 2060079 15 chr1 2060079 2060089 16 chr1 2060089 2060099 17 chr1 2060099 2060109 18 chr1 2060109 2060119 19 chr1 2060119 2060129 20 chr1 2060129 2060139 21 chr1 2060139 2060149 22 chr1 2060149 2060159 23 chr1 2060159 2060169 24 chr1 2060169 2060179 25 chr1 2060179 2060187 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp3fpddxy3/f1.bed) bedtools_df Chromosome Start End 0 chr2 65537 65547 1 chr2 65547 65557 2 chr2 65557 65567 3 chr2 65567 65577 4 chr2 65577 65587 ... ... ... ... 1866 chr2 3533192 3533202 1867 chr2 3533202 3533212 1868 chr2 3533212 3533222 1869 chr2 3533222 3533232 1870 chr2 3533232 3533242 [1871 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmppkkd8q6a/f1.bed) bedtools_df Chromosome Start End 0 chr1 5993521 5993531 1 chr1 5993531 5993541 2 chr1 5993541 5993551 3 chr1 5993551 5993561 4 chr1 5993561 5993571 .. ... ... ... 388 chr1 5997401 5997411 389 chr1 5997411 5997421 390 chr1 5997421 5997431 391 chr1 5997431 5997441 392 chr1 5997441 5997448 [393 rows x 3 columns] bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpd7bd5a0l/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp6wqi5kom/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp5bcycl08/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp2wl5kwvo/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmpo6nx5k2g/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp7t3_76sb/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 bedtools makewindows -w 10 -b <(sort -k1,1 -k2,2n /tmp/tmp8cqo7_bb/f1.bed) bedtools_df Chromosome Start End 0 chr1 1 2 =============================== warnings summary =============================== tests/conftest.py:83 /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/conftest.py:83: DeprecationWarning: invalid escape sequence '\s' sep="\s+", .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 1291 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:349: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only. bedtools_df = bedtools_df.drop("Chromosome2", 1) .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 1055 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:544: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only. bedtools_df = bedtools_df.drop("Chromosome2", 1) .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/methods/concat.py:47: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/multioverlap.py:155: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` df.loc[:, names] = df[names].astype(np.int32) .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 34 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:119: FutureWarning: The squeeze argument has been deprecated and will be removed in a future version. Append .squeeze("columns") to the call to squeeze. bedtools_df = pd.read_csv( .pybuild/cpython3_3.11_pyranges/build/tests/test_genomicfeatures.py::test_introns_single /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_genomicfeatures.py:40: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` x.loc[:, "Start"] = x.Start.astype(int) .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 17 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:251: FutureWarning: The squeeze argument has been deprecated and will be removed in a future version. Append .squeeze("columns") to the call to squeeze. bedtools_df = pd.read_csv( .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 2000 warnings /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:193: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` expected.loc[:, "Cluster"] = expected.Cluster.astype(np.int32) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_binary.py::test_set_intersect[False] - Exception: Starts/En... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain2-method_chain2] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain35-method_chain35] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain3-method_chain3] FAILED tests/test_binary.py::test_set_intersect[same] - Exception: Starts/End... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain36-method_chain36] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain4-method_chain4] FAILED tests/test_binary.py::test_nearest[downstream-False-opposite] - ValueE... FAILED tests/test_binary.py::test_set_union[False] - Exception: Starts/Ends n... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain5-method_chain5] FAILED tests/test_binary.py::test_jaccard[False] - Exception: Starts/Ends not... FAILED tests/test_binary.py::test_set_union[same] - Exception: Starts/Ends no... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain37-method_chain37] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain6-method_chain6] FAILED tests/test_binary.py::test_jaccard[same] - Exception: Starts/Ends not ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain7-method_chain7] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain8-method_chain8] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain38-method_chain38] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain9-method_chain9] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain10-method_chain10] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain39-method_chain39] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain11-method_chain11] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain12-method_chain12] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain40-method_chain40] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain13-method_chain13] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain41-method_chain41] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain14-method_chain14] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain42-method_chain42] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain15-method_chain15] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain43-method_chain43] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain45-method_chain45] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain19-method_chain19] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain47-method_chain47] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain21-method_chain21] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain49-method_chain49] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain22-method_chain22] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain50-method_chain50] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain51-method_chain51] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain52-method_chain52] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain23-method_chain23] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain53-method_chain53] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain54-method_chain54] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain55-method_chain55] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain24-method_chain24] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain56-method_chain56] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain57-method_chain57] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain25-method_chain25] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain58-method_chain58] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain59-method_chain59] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain60-method_chain60] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain26-method_chain26] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain61-method_chain61] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain62-method_chain62] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain27-method_chain27] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain63-method_chain63] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain28-method_chain28] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain64-method_chain64] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain29-method_chain29] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain66-method_chain66] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain31-method_chain31] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain68-method_chain68] FAILED tests/test_binary.py::test_k_nearest[downstream-False-opposite-last] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain33-method_chain33] FAILED tests/test_binary.py::test_k_nearest[downstream-False-same-last] - Val... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain70-method_chain70] FAILED tests/test_binary.py::test_k_nearest[downstream-False-False-last] - Va... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain71-method_chain71] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain117-method_chain117] FAILED tests/test_binary.py::test_k_nearest[downstream-True-opposite-last] - ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain72-method_chain72] FAILED tests/test_binary.py::test_k_nearest[downstream-True-same-last] - Valu... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain119-method_chain119] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain73-method_chain73] FAILED tests/test_binary.py::test_k_nearest[downstream-True-False-last] - Val... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain74-method_chain74] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain120-method_chain120] FAILED tests/test_binary.py::test_k_nearest[upstream-False-opposite-last] - V... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain75-method_chain75] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain121-method_chain121] FAILED tests/test_binary.py::test_k_nearest[upstream-False-same-last] - Value... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain76-method_chain76] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain122-method_chain122] FAILED tests/test_binary.py::test_k_nearest[upstream-False-False-last] - Valu... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain77-method_chain77] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain123-method_chain123] FAILED tests/test_binary.py::test_coverage[False] - Exception: Starts/Ends no... FAILED tests/test_binary.py::test_k_nearest[upstream-True-opposite-last] - Va... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain78-method_chain78] FAILED tests/test_binary.py::test_coverage[same] - Exception: Starts/Ends not... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain124-method_chain124] FAILED tests/test_binary.py::test_coverage[opposite] - Exception: Starts/Ends... FAILED tests/test_binary.py::test_k_nearest[upstream-True-same-last] - ValueE... FAILED tests/test_binary.py::test_subtraction[same] - Exception: Starts/Ends ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain125-method_chain125] FAILED tests/test_binary.py::test_subtraction[opposite] - Exception: Starts/E... FAILED tests/test_binary.py::test_k_nearest[upstream-True-False-last] - Value... FAILED tests/test_binary.py::test_subtraction[False] - Exception: Starts/Ends... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain126-method_chain126] FAILED tests/test_binary.py::test_k_nearest[None-False-opposite-last] - Value... FAILED tests/test_binary.py::test_nearest[None-True-False] - AssertionError: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain127-method_chain127] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain82-method_chain82] FAILED tests/test_binary.py::test_k_nearest[None-False-same-last] - ValueErro... FAILED tests/test_binary.py::test_nearest[None-True-same] - AssertionError: A... FAILED tests/test_binary.py::test_k_nearest[None-False-False-last] - ValueErr... FAILED tests/test_binary.py::test_nearest[None-True-opposite] - ValueError: B... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain84-method_chain84] FAILED tests/test_binary.py::test_k_nearest[None-True-opposite-last] - ValueE... FAILED tests/test_binary.py::test_nearest[None-False-False] - ValueError: Buf... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain85-method_chain85] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain129-method_chain129] FAILED tests/test_binary.py::test_k_nearest[None-True-same-last] - ValueError... FAILED tests/test_binary.py::test_nearest[None-False-same] - ValueError: Buff... FAILED tests/test_binary.py::test_k_nearest[None-True-False-last] - ValueErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain86-method_chain86] FAILED tests/test_binary.py::test_k_nearest_1_vs_nearest - ValueError: Buffer... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain0-method_chain0] FAILED tests/test_binary.py::test_nearest[None-False-opposite] - ValueError: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain131-method_chain131] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain87-method_chain87] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain1-method_chain1] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain158-method_chain158] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain159-method_chain159] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain88-method_chain88] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain133-method_chain133] FAILED tests/test_binary.py::test_nearest[upstream-True-False] - AssertionErr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain160-method_chain160] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain134-method_chain134] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain89-method_chain89] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain161-method_chain161] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain135-method_chain135] FAILED tests/test_binary.py::test_nearest[upstream-True-same] - AssertionErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain90-method_chain90] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain162-method_chain162] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain136-method_chain136] FAILED tests/test_binary.py::test_nearest[upstream-True-opposite] - Assertion... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain91-method_chain91] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain137-method_chain137] FAILED tests/test_binary.py::test_nearest[upstream-False-False] - ValueError:... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain92-method_chain92] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain138-method_chain138] FAILED tests/test_binary.py::test_nearest[upstream-False-same] - ValueError: ... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain166-method_chain166] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain139-method_chain139] FAILED tests/test_binary.py::test_nearest[upstream-False-opposite] - ValueErr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain140-method_chain140] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain96-method_chain96] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain168-method_chain168] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain141-method_chain141] FAILED tests/test_binary.py::test_nearest[downstream-True-False] - AssertionE... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain98-method_chain98] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain169-method_chain169] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain99-method_chain99] FAILED tests/test_binary.py::test_nearest[downstream-True-same] - AssertionEr... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain100-method_chain100] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain101-method_chain101] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain102-method_chain102] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain170-method_chain170] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain103-method_chain103] FAILED tests/test_binary.py::test_nearest[downstream-True-opposite] - Asserti... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain145-method_chain145] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain104-method_chain104] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain105-method_chain105] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain171-method_chain171] FAILED tests/test_binary.py::test_nearest[downstream-False-False] - ValueErro... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain106-method_chain106] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain147-method_chain147] FAILED tests/test_binary.py::test_nearest[downstream-False-same] - ValueError... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain107-method_chain107] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain148-method_chain148] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain108-method_chain108] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain172-method_chain172] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain149-method_chain149] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain109-method_chain109] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain150-method_chain150] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain196-method_chain196] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain110-method_chain110] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain151-method_chain151] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain197-method_chain197] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain111-method_chain111] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain152-method_chain152] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain198-method_chain198] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain173-method_chain173] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain153-method_chain153] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain199-method_chain199] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain154-method_chain154] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain112-method_chain112] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain200-method_chain200] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain155-method_chain155] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain174-method_chain174] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain201-method_chain201] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain156-method_chain156] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain113-method_chain113] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain202-method_chain202] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain157-method_chain157] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain203-method_chain203] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain175-method_chain175] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain204-method_chain204] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain205-method_chain205] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain176-method_chain176] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain206-method_chain206] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain229-method_chain229] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain115-method_chain115] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain207-method_chain207] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain256-method_chain256] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain208-method_chain208] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain257-method_chain257] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain209-method_chain209] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain231-method_chain231] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain258-method_chain258] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain232-method_chain232] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain178-method_chain178] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain259-method_chain259] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain210-method_chain210] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain233-method_chain233] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain211-method_chain211] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain260-method_chain260] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain180-method_chain180] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain234-method_chain234] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain182-method_chain182] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain183-method_chain183] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain235-method_chain235] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain262-method_chain262] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain184-method_chain184] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain215-method_chain215] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain236-method_chain236] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain264-method_chain264] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain185-method_chain185] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain237-method_chain237] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain186-method_chain186] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain238-method_chain238] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain217-method_chain217] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain266-method_chain266] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain187-method_chain187] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain239-method_chain239] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain218-method_chain218] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain267-method_chain267] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain188-method_chain188] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain219-method_chain219] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain268-method_chain268] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain189-method_chain189] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain220-method_chain220] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain269-method_chain269] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain190-method_chain190] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain243-method_chain243] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain221-method_chain221] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain270-method_chain270] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain222-method_chain222] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain245-method_chain245] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain271-method_chain271] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain246-method_chain246] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain223-method_chain223] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain247-method_chain247] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain272-method_chain272] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain248-method_chain248] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain194-method_chain194] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain224-method_chain224] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain249-method_chain249] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain273-method_chain273] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain281-method_chain281] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain250-method_chain250] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain251-method_chain251] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain225-method_chain225] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain274-method_chain274] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain282-method_chain282] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain252-method_chain252] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain253-method_chain253] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain254-method_chain254] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain255-method_chain255] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain283-method_chain283] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain303-method_chain303] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain304-method_chain304] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain322-method_chain322] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain284-method_chain284] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain305-method_chain305] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain276-method_chain276] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain306-method_chain306] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain323-method_chain323] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain307-method_chain307] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain285-method_chain285] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain286-method_chain286] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain278-method_chain278] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain308-method_chain308] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain280-method_chain280] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain309-method_chain309] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain287-method_chain287] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain327-method_chain327] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain288-method_chain288] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain339-method_chain339] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain329-method_chain329] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain330-method_chain330] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain311-method_chain311] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain341-method_chain341] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain331-method_chain331] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain292-method_chain292] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain343-method_chain343] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain332-method_chain332] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain313-method_chain313] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain344-method_chain344] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain345-method_chain345] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain294-method_chain294] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain333-method_chain333] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain346-method_chain346] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain295-method_chain295] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain347-method_chain347] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain296-method_chain296] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain348-method_chain348] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain297-method_chain297] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain334-method_chain334] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain349-method_chain349] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain298-method_chain298] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain315-method_chain315] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain350-method_chain350] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain299-method_chain299] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain351-method_chain351] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain300-method_chain300] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain335-method_chain335] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain352-method_chain352] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain301-method_chain301] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain353-method_chain353] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain302-method_chain302] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain336-method_chain336] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain316-method_chain316] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain354-method_chain354] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain355-method_chain355] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain337-method_chain337] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain356-method_chain356] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain367-method_chain367] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain317-method_chain317] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain378-method_chain378] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain357-method_chain357] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain379-method_chain379] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain368-method_chain368] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain318-method_chain318] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain358-method_chain358] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain380-method_chain380] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain369-method_chain369] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain319-method_chain319] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain381-method_chain381] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain382-method_chain382] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain370-method_chain370] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain320-method_chain320] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain360-method_chain360] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain383-method_chain383] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain371-method_chain371] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain384-method_chain384] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain321-method_chain321] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain372-method_chain372] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain362-method_chain362] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain385-method_chain385] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain386-method_chain386] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain388-method_chain388] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain396-method_chain396] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain374-method_chain374] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain364-method_chain364] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain397-method_chain397] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain398-method_chain398] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain390-method_chain390] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain399-method_chain399] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain400-method_chain400] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain365-method_chain365] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain401-method_chain401] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain376-method_chain376] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain392-method_chain392] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain402-method_chain402] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain393-method_chain393] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain394-method_chain394] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain366-method_chain366] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain395-method_chain395] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain403-method_chain403] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain411-method_chain411] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain416-method_chain416] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain404-method_chain404] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain421-method_chain421] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain405-method_chain405] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain406-method_chain406] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain417-method_chain417] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain413-method_chain413] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain423-method_chain423] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain407-method_chain407] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain418-method_chain418] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain414-method_chain414] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain425-method_chain425] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain419-method_chain419] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain427-method_chain427] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain429-method_chain429] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain415-method_chain415] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain428-method_chain428] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain420-method_chain420] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain430-method_chain430] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain432-method_chain432] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain435-method_chain435] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain431-method_chain431] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain439-method_chain439] FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain433-method_chain433] FAILED tests/test_unary.py::test_merge[True] - Exception: Starts/Ends not int... FAILED tests/test_unary.py::test_merge[False] - Exception: Starts/Ends not in... FAILED tests/test_unary.py::test_cluster[False] - Exception: Starts/Ends not ... FAILED tests/test_genomicfeatures.py::test_introns_single - ValueError: Buffe... FAILED tests/test_do_not_error.py::test_three_in_a_row[strandedness_chain434-method_chain434] FAILED tests/test_unary.py::test_cluster[True] - Exception: Starts/Ends not i... FAILED tests/test_unary.py::test_summary - Exception: Starts/Ends not int64 o... FAILED tests/windows/test_windows.py::test_windows - ValueError: Buffer dtype... FAILED tests/windows/test_windows.py::test_windows2 - ValueError: Buffer dtyp... FAILED tests/test_unary.py::test_windows - Exception: Starts/Ends not int64 o... ======== 405 failed, 126 passed, 4407 warnings in 37442.68s (10:24:02) ========= E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build; python3.11 -m pytest -n 4 dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13 make: *** [debian/rules:14: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3880 and its subdirectories