I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 2 13:00:34 -12 2023 I: pbuilder-time-stamp: 1672707634 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [cnvkit_0.9.5-3.dsc] I: copying [./cnvkit_0.9.5.orig.tar.gz] I: copying [./cnvkit_0.9.5-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Mar 27 22:43:40 2019 -12 gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438 gpgv: issuer "osallou@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.5-3.dsc dpkg-source: info: extracting cnvkit in cnvkit-0.9.5 dpkg-source: info: unpacking cnvkit_0.9.5.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.5-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-py-ext dpkg-source: info: applying python3compat.patch dpkg-source: info: applying spelling dpkg-source: info: applying controldir I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1105190/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2642de1da2c741bbabdb20b099dad18c' 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='1105190' 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/tmp.RcEykp4YkN/pbuilderrc_ujLs --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RcEykp4YkN/b1 --logfile b1/build.log cnvkit_0.9.5-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 10 16:21 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/1105190/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: amd64 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 (>= 11~), dh-python, python3-all, python3-setuptools, python3-pyfaidx, help2man, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pyvcf, python3-future, r-bioc-dnacopy, poppler-utils dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pyvcf; however: Package python3-pyvcf is not installed. pbuilder-satisfydepends-dummy depends on python3-future; however: Package python3-future is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-dnacopy; however: Package r-bioc-dnacopy is not installed. pbuilder-satisfydepends-dummy depends on poppler-utils; however: Package poppler-utils 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} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcairo2{a} libcroco3{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts2{a} libice6{a} libicu63{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpoppler82{a} libpsl5{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libssl1.1{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6{a} lsb-base{a} m4{a} man-db{a} mime-support{a} openssl{a} po-debconf{a} poppler-utils{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-biopython{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-distutils{a} python3-future{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pysam{a} python3-pyvcf{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-tz{a} python3.7{a} python3.7-minimal{a} r-base-core{a} r-bioc-dnacopy{a} readline-common{a} sensible-utils{a} ttf-bitstream-vera{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx ncbi-blast+ poppler-data publicsuffix python-biopython-doc python3-bs4 python3-html5lib python3-lxml python3-numexpr python3-olefile python3-renderpm python3-tables python3-tk r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After unpacking 329 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 fonts-lyx all 2.3.2-1 [199 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u1 [63.7 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libopenjp2-7 amd64 2.3.0-2+deb10u2 [158 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u2 [271 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libpoppler82 amd64 0.71.0-5 [1507 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 poppler-utils amd64 0.71.0-5 [184 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 python-matplotlib-data all 3.0.2-2 [4138 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 python3-all amd64 3.7.3-1 [1068 B] Get: 130 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 python3-reportlab-accel amd64 3.5.13-1+deb10u1 [35.3 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 python3-pil amd64 5.4.1-2+deb10u2 [395 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 python3-reportlab all 3.5.13-1+deb10u1 [541 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 python3-biopython amd64 1.73+dfsg-1 [1287 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 [15.7 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 python3-cycler all 0.10.0-1 [7556 B] Get: 138 http://deb.debian.org/debian buster/main amd64 python3-dateutil all 2.7.3-3 [64.5 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 python3-decorator all 4.3.0-1.1 [14.5 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 python3-future all 0.16.0-1 [346 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 python3-kiwisolver amd64 1.0.1-2+b1 [65.4 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 python3-matplotlib amd64 3.0.2-2 [5353 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 python3-tz all 2019.1-1 [27.1 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 python3-pandas-lib amd64 0.23.3+dfsg-3 [3475 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 python3-pandas all 0.23.3+dfsg-3 [1750 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 python3-pyfaidx all 0.5.5.2-1 [25.3 kB] Get: 148 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get: 149 http://deb.debian.org/debian buster/main amd64 python3-pyvcf amd64 0.6.8+git20170215.476169c-1 [54.8 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 python3-scipy amd64 1.1.0-7 [10.0 MB] Get: 151 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 zip amd64 3.0-11+b1 [234 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get: 154 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get: 156 http://deb.debian.org/debian buster/main amd64 r-bioc-dnacopy amd64 1.56.0-1 [419 kB] Fetched 103 MB in 2s (68.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../06-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../07-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../08-libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../09-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../10-python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... 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 ... 20105 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../2-libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../4-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../5-libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../6-python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... 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 ... 20566 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../006-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../007-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../008-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../009-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../010-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../011-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../012-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package openssl. Preparing to unpack .../013-openssl_1.1.1d-0+deb10u7_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u7) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../014-ca-certificates_20200601~deb10u2_all.deb ... Unpacking ca-certificates (20200601~deb10u2) ... Selecting previously unselected package libtool. 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Unpacking r-bioc-dnacopy (1.56.0-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libgraphite2-3:amd64 (1.3.13-7) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libpixman-1-0:amd64 (0.36.0-1) ... Setting up lsb-base (10.2019051400) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up mime-support (3.62) ... Setting up libdatrie1:amd64 (0.2.12-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.2-1) ... Setting up unzip (6.0-23+deb10u2) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up zip (3.0-11+b1) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u2) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libfribidi0:amd64 (1.0.5-3.1+deb10u1) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up libtcl8.6:amd64 (8.6.9+dfsg-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libopenjp2-7:amd64 (2.3.0-2+deb10u2) ... Setting up libthai-data (0.1.28-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up python-matplotlib-data (3.0.2-2) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up xdg-utils (1.1.3-1+deb10u1) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libtool (2.4.6-9) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up help2man (1.47.8) ... Setting up libthai0:amd64 (0.1.28-2) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libcurl4:amd64 (7.64.0-4+deb10u2) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:amd64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up libpaper-utils (1.1.28) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-tz (2019.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up python3-pil:amd64 (5.4.1-2+deb10u2) ... Setting up python3-decorator (4.3.0-1.1) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up python3-reportlab (3.5.13-1+deb10u1) ... Setting up python3-dateutil (2.7.3-3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up python3-pyfaidx (0.5.5.2-1) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:amd64 (8.6.9-2) ... Setting up libpango-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libpoppler82:amd64 (0.71.0-5) ... Setting up python3-all (3.7.3-1) ... Setting up libcairo2:amd64 (1.16.0-4+deb10u1) ... Setting up python3-pyvcf (0.6.8+git20170215.476169c-1) ... Setting up python3-kiwisolver (1.0.1-2+b1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up poppler-utils (0.71.0-5) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up python3-future (0.16.0-1) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-biopython (1.73+dfsg-1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up python3-matplotlib (3.0.2-2) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up python3-scipy (1.1.0-7) ... Setting up python3-pandas-lib (0.23.3+dfsg-3) ... Setting up python3-pandas (0.23.3+dfsg-3) ... Setting up r-base-core (3.5.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-bioc-dnacopy (1.56.0-1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/cnvkit-0.9.5/ && 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 > ../cnvkit_0.9.5-3_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.5-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Olivier Sallou dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/cnvkit-0.9.5' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.5/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-0.9.5/test' if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:217: python3.7 setup.py clean running clean removing '/build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info make[1]: Leaving directory '/build/cnvkit-0.9.5' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --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:217: python3.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/cnvkit-0.9.5' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_build I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/commands.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/ztest.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/vary.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/target.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/rna.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/reports.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/reference.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/plots.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/params.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/importers.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/fix.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/export.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/core.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/call.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/batch.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/access.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/_version.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/subtract.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/subdivide.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/merge.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/intersect.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/gary.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/combiners.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/chromsort.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.7 copying and adjusting ./cnvkit -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-skg_convert -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-reference2targets -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-guess_baits -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_ztest -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_updater -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_annotate -> build/scripts-3.7 copying ./scripts/snpfilter.sh -> build/scripts-3.7 changing mode of build/scripts-3.7/cnvkit from 644 to 755 changing mode of build/scripts-3.7/cnvkit-skg_convert from 644 to 755 changing mode of build/scripts-3.7/cnvkit-reference2targets from 644 to 755 changing mode of build/scripts-3.7/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.7/cnvkit-cnv_ztest from 644 to 755 changing mode of build/scripts-3.7/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.7/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.7/cnvkit-cnv_annotate from 644 to 755 cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-0.9.5' debian/rules override_dh_auto_test make[1]: Entering directory '/build/cnvkit-0.9.5' cd test && /usr/bin/make -j16 make[2]: Entering directory '/build/cnvkit-0.9.5/test' python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-20_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Created directory build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn Number of target and antitarget files: 3, 3 No FASTA reference genome provided; skipping GC, RM calculations Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=67.2 x 0.532 = 35.7) --> assuming male Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=38.7 x 0.532 = 20.6) --> assuming male Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=94.8 x 0.532 = 50.4) --> assuming male Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=6.53 x 0.809 = 5.28) --> assuming male Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=9.76 x 0.895 = 8.74) --> assuming male Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=18.1 x 0.895 = 16.2) --> assuming male Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Calculating average bin coverages Calculating bin spreads Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 89 (1.3392%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) NOTCH2 chr1:120572470-120572622 log2=-2.599 spread=1.522 GAK chr4:896278-896357 log2=-1.523 spread=1.267 MAP3K1 chr5:56111354-56111894 log2=-1.492 spread=1.060 FLT4 chr5:180076418-180076603 log2=-2.232 spread=1.421 DOM3Z chr6:31938905-31939081 log2=-20.033 spread=0.045 " chr6:31939599-31940313 log2=-19.608 spread=0.181 STK19 chr6:31940351-31940562 log2=-19.003 spread=0.189 " chr6:31946632-31946824 log2=-20.060 spread=0.088 " chr6:31947142-31947366 log2=-20.128 spread=0.065 " chr6:31948176-31948360 log2=-19.992 spread=0.148 " chr6:31948382-31948612 log2=-19.780 spread=0.162 " chr6:31948730-31949253 log2=-20.063 spread=0.020 NOTCH4 chr6:32163159-32163956 log2=-19.331 spread=0.202 " chr6:32164046-32164227 log2=-19.777 spread=0.180 " chr6:32164652-32164888 log2=-19.995 spread=0.151 " chr6:32165021-32165403 log2=-19.643 spread=0.195 " chr6:32166163-32166545 log2=-20.057 spread=0.076 " chr6:32166648-32166962 log2=-3.526 spread=5.774 " chr6:32168554-32168821 log2=-19.621 spread=0.193 " chr6:32168844-32169306 log2=-19.700 spread=0.164 " chr6:32169801-32170391 log2=-19.433 spread=0.206 " chr6:32171492-32171691 log2=-20.108 spread=0.103 " chr6:32171861-32172198 log2=-3.146 spread=7.284 " chr6:32178478-32178749 log2=-19.934 spread=0.167 " chr6:32180197-32180441 log2=-10.912 spread=9.531 " chr6:32180544-32180722 log2=-19.700 spread=0.182 " chr6:32180857-32181062 log2=-19.591 spread=0.214 " chr6:32181411-32181646 log2=-19.979 spread=0.168 " chr6:32181832-32182066 log2=-19.971 spread=0.174 " chr6:32182948-32183194 log2=-19.947 spread=0.171 " chr6:32184667-32185079 log2=-19.931 spread=0.162 " chr6:32185720-32185919 log2=-19.724 spread=0.192 " chr6:32187317-32187601 log2=-19.783 spread=0.171 " chr6:32187871-32188094 log2=-19.686 spread=0.190 " chr6:32188127-32188451 log2=-19.636 spread=0.165 " chr6:32188481-32188693 log2=-19.906 spread=0.130 " chr6:32188704-32189133 log2=-19.522 spread=0.199 " chr6:32190258-32190616 log2=-19.586 spread=0.207 " chr6:32190724-32190908 log2=-19.562 spread=0.218 " chr6:32191570-32191668 log2=-19.792 spread=0.174 " chr6:32191676-32191753 log2=-19.393 spread=0.201 CGH chr7:52520101-52520286 log2=-1.534 spread=1.178 SMO chr7:128828938-128829041 log2=-2.070 spread=1.324 GPR124 chr8:37654740-37655077 log2=-1.623 spread=1.026 GPSM1 chr9:139222089-139222248 log2=-4.896 spread=2.116 MRC1 chr10:18136438-18136613 log2=-1.967 spread=3.254 RET chr10:43572644-43572830 log2=-1.394 spread=1.097 FLT3 chr13:28674525-28674708 log2=-2.268 spread=1.749 IRS2 chr13:110438332-110438432 log2=-3.655 spread=2.330 CGH chr14:19220933-19221047 log2=-1.234 spread=1.211 MAP3K9 chr14:71275790-71275923 log2=-2.828 spread=1.943 LTK chr15:41803310-41803809 log2=-1.970 spread=1.452 PDPK1 chr16:2588022-2588201 log2=-1.783 spread=1.088 " chr16:2611404-2611585 log2=-5.189 spread=1.939 " chr16:2611721-2611943 log2=-11.822 spread=9.176 " chr16:2615504-2615725 log2=-20.129 spread=0.003 " chr16:2616307-2616486 log2=-20.077 spread=0.072 " chr16:2631267-2631414 log2=-20.027 spread=0.061 " chr16:2631583-2631734 log2=-20.122 spread=0.087 " chr16:2633363-2633616 log2=-20.108 spread=0.092 BOLA2B chr16:29466011-29466278 log2=-19.007 spread=0.177 MAP2K4 chr17:11924151-11924355 log2=-2.111 spread=1.902 GIPC3 chr19:3585549-3585853 log2=-1.530 spread=1.093 INSR chr19:7293751-7294042 log2=-2.032 spread=1.542 NOTCH3 chr19:15311544-15311749 log2=-1.901 spread=1.207 CD79A chr19:42384673-42384848 log2=-1.888 spread=1.229 CRLF2 chrX:1314835-1315039 log2=-20.125 spread=0.029 " chrX:1317372-1317594 log2=-20.136 spread=0.045 " chrX:1321225-1321435 log2=-19.869 spread=0.196 " chrX:1325274-1325530 log2=-20.131 spread=0.012 " chrX:1327651-1327830 log2=-20.012 spread=0.030 " chrX:1331391-1331576 log2=-20.024 spread=0.051 CGH chrY:2654543-2654722 log2=-4.357 spread=4.442 " chrY:3023482-3023672 log2=-4.960 spread=6.784 " chrY:4564417-4564597 log2=-11.686 spread=9.039 " chrY:7540620-7540741 log2=-5.016 spread=6.755 " chrY:9008607-9008759 log2=-12.124 spread=8.796 " chrY:13131970-13132039 log2=-20.071 spread=0.102 " chrY:13199435-13199623 log2=-4.281 spread=6.165 " chrY:15007107-15007258 log2=-6.946 spread=7.403 " chrY:16504318-16504496 log2=-5.090 spread=6.641 " chrY:18022729-18022918 log2=-5.529 spread=6.991 " chrY:19506485-19506650 log2=-11.896 spread=8.895 " chrY:21033918-21034071 log2=-20.101 spread=0.087 " chrY:22554204-22554385 log2=-6.070 spread=7.225 " chrY:24000593-24000773 log2=-4.446 spread=4.603 " chrY:28462977-28463157 log2=-5.435 spread=7.074 " chrY:28463435-28463622 log2=-11.305 spread=9.238 " chrY:28514033-28514208 log2=-12.104 spread=8.739 Antitargets: 111 (0.8835%) bins failed filters Wrote build/reference-picard.cnn with 19209 regions python3 ../cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr python3 ../cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr python3 ../cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr python3 ../cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr python3 ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr python3 ../cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr python3 ../cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr Processing target: p2-20_5 Processing target: p2-20_3 Keeping 6557 of 6646 bins Processing target: p2-20_2 Correcting for GC bias... Correcting for density bias... Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Keeping 6557 of 6646 bins Processing target: p2-5_5 Processing antitarget: p2-20_5 Correcting for GC bias... Processing target: p2-20_4 Processing antitarget: p2-20_2 Keeping 12452 of 12563 bins Keeping 6557 of 6646 bins Correcting for density bias... Correcting for GC bias... Keeping 12452 of 12563 bins Correcting for GC bias... Correcting for density bias... WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... Keeping 6557 of 6646 bins Correcting for GC bias... Processing antitarget: p2-5_5 Correcting for density bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.60 x more variable than antitargets Processing antitarget: p2-20_3 Processing target: p2-9_2 Processing target: p2-20_1 Keeping 12452 of 12563 bins Processing antitarget: p2-20_4 Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Keeping 12452 of 12563 bins Keeping 12452 of 12563 bins Targets are 1.04 x more variable than antitargets Keeping 6557 of 6646 bins Keeping 6557 of 6646 bins Correcting for GC bias... Wrote build/p2-20_5.cnr with 19009 regions Correcting for GC bias... Targets are 1.09 x more variable than antitargets Correcting for GC bias... Correcting for GC bias... Correcting for density bias... WARNING: Skipping correction for RepeatMasker bias Correcting for density bias... WARNING: Skipping correction for RepeatMasker bias Processing antitarget: p2-20_1 python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns Wrote build/p2-5_5.cnr with 19009 regions Antitargets are 1.01 x more variable than targets Keeping 12452 of 12563 bins Correcting for GC bias... Targets are 1.18 x more variable than antitargets Processing antitarget: p2-9_2 python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf Wrote build/p2-20_2.cnr with 19009 regions WARNING: Skipping correction for RepeatMasker bias Wrote build/p2-20_3.cnr with 19009 regions Targets are 1.08 x more variable than antitargets python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf Keeping 12452 of 12563 bins python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Wrote build/p2-20_1.cnr with 19009 regions Wrote build/p2-20_4.cnr with 19009 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf Targets are 1.34 x more variable than antitargets python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Wrote build/p2-9_2.cnr with 19009 regions Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-5_5 as male Treating sample p2-20_2 as male Treating sample p2-20_1 as male Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Selected test sample NA12882 and control sample NA12878 Treating sample p2-9_2 as male Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Wrote p2-9_2.nexus /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Dropped 1 / 966 bins on chromosome chr6 /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-20_5.cns with 64 regions python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-20_2.cns with 77 regions Wrote build/p2-5_5.cns with 49 regions python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns python3 ../cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-20_3.cns with 48 regions python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Dropped 1 / 5 bins on chromosome chrY Treating sample p2-20_2 as male /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-20_4.cns with 65 regions Wrote p2-20_2-cbs-diagram.pdf Treating sample p2-20_5 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_5.call.cns with 64 regions Treating sample p2-20_2 as male python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-9_2.cns with 57 regions python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns Treating sample p2-20_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 77 regions Wrote build/p2-20_1.cns with 78 regions python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem Treating sample p2-5_5 as male Wrote p2-5_5-cbs-diagram.pdf Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ --ci -b 50 -a 0.5 python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Treating sample p2-5_5 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 49 regions Treating sample p2-20_3 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 48 regions Treating sample p2-20_4 as male python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Rescaling sample with purity 0.65, ploidy 2 Treating sample p2-5_5 as male Wrote build/p2-20_4.call.cns with 65 regions python3 ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf Wrote p2-20_2-diagram.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf Wrote p2-9_2.theta2.input python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf Wrote p2-5_5-metrics.tsv python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf Wrote p2-5_5-segmetrics.cns with 49 regions Wrote p2-9_2-metrics.tsv python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf Wrote p2-20_1-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf Wrote p2-9_2-segmetrics.cns with 57 regions python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf /build/cnvkit-0.9.5/cnvlib/export.py:70: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. ("GWEIGHT", 1), Wrote p2-all.cdt Wrote p2-9_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf python3 ../cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf Showing 1498 probes and 0 selected genes in region chr1 Showing 341 probes and 14 selected genes in region chr9:149999-45000000 Placed 727 variants into 19009 bins Wrote p2-9_2.nexus-ogt Showing 186 probes and 2 selected genes in region chr9:0-14504268 Wrote p2-9_2-chr9p-scatter.pdf python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt Treating sample p2-9_2 as male python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt Wrote p2-all-jtv.txt Wrote p2-20-metrics.tsv Treating sample p2-20_1 as male Wrote p2-9_2-cbs-diagram.pdf Detected file format: bed Showing 43 probes and 1 selected genes in region chr9:2000000-4000000 Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf Wrote p2-9_2-chr1-scatter.pdf python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt python3 ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg Wrote p2-20_1-cbs-diagram.pdf Showing 54 probes and 1 selected genes in region chr9:8000000-12000000 Wrote p2-5_5-scatter.pdf python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns Treating sample p2-9_2 as male Treating sample p2-5_5 as male Treating sample p2-9_2 as male Treating sample p2-20_1 as male Treating sample p2-20_2 as male Treating sample p2-20_3 as male Treating sample p2-20_4 as male Treating sample p2-20_5 as male Treating sample p2-20_1 as male Found 1 gene breakpoints Wrote p2-9_2-breaks.txt Treating sample p2-9_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 57 regions Treating sample p2-20_1 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 78 regions Wrote p2-all.seg python3 ../cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed python3 ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf Treating sample p2-9_2 as male Wrote gender-picard.txt Wrote p2-20_2-both-diagram.pdf Treating sample p2-5_5.call as male Treating sample p2-9_2.call as male Treating sample p2-20_1.call as male Treating sample p2-20_2.call as male Treating sample p2-20_3.call as male Treating sample p2-20_4.call as male Treating sample p2-20_5.call as male Wrote p2-all.bed Wrote heatmap-picard.pdf Wrote p2-9_2-scatter.pdf Treating sample p2-9_2.call as male which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf Wrote p2-5_5-both-diagram.pdf /usr/bin/pdfunite Wrote p2-9_2.vcf Found 322 gene-level gains and losses Wrote p2-9_2-genemetrics.txt Wrote p2-9_2-both-diagram.pdf Wrote p2-20_1-both-diagram.pdf which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf /usr/bin/pdfunite make[2]: Leaving directory '/build/cnvkit-0.9.5/test' cd test && /usr/bin/make -j16 clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.5/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-0.9.5/test' rm -Rf test/build test/*.tsv make[1]: Leaving directory '/build/cnvkit-0.9.5' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/cnvkit-0.9.5' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_install I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/cnvkit-0.9.5/debian/cnvkit running install running build running build_py running build_scripts running install_lib creating /build/cnvkit-0.9.5/debian/cnvkit/usr creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7 creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/bedio.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/genepred.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/gff.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/picard.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/seg.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/tab.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/util.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/chromsort.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/combiners.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/gary.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/intersect.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/merge.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/rangelabel.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/subdivide.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/subtract.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/none.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/_version.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/access.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/antitarget.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/autobin.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/batch.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/call.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/cmdutil.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/cnary.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/core.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/coverage.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/descriptives.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/diagram.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/export.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/fix.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/heatmap.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/import_rna.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/importers.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/metrics.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/parallel.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/params.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/plots.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/reference.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/reports.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/rna.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/samutil.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/scatter.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segfilters.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmetrics.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/smoothing.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/target.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/vary.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/ztest.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/commands.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/gff.py to gff.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/picard.py to picard.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/seg.py to seg.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/tab.py to tab.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/util.py to util.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/chromsort.py to chromsort.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/combiners.py to combiners.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/gary.py to gary.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/intersect.py to intersect.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/merge.py to merge.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/subdivide.py to subdivide.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/subtract.py to subtract.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/none.py to none.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/_version.py to _version.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/access.py to access.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/antitarget.py to antitarget.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/autobin.py to autobin.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/batch.py to batch.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/call.py to call.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/cnary.py to cnary.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/core.py to core.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/coverage.py to coverage.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/descriptives.py to descriptives.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/diagram.py to diagram.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/export.py to export.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/fix.py to fix.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/heatmap.py to heatmap.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/import_rna.py to import_rna.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/importers.py to importers.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/metrics.py to metrics.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/parallel.py to parallel.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/params.py to params.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/plots.py to plots.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/reference.py to reference.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/reports.py to reports.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/rna.py to rna.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/samutil.py to samutil.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/scatter.py to scatter.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segfilters.py to segfilters.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/smoothing.py to smoothing.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/target.py to target.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/vary.py to vary.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/ztest.py to ztest.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/commands.py to commands.cpython-37.pyc running install_egg_info running egg_info creating CNVkit.egg-info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt writing manifest file 'CNVkit.egg-info/SOURCES.txt' reading manifest file 'CNVkit.egg-info/SOURCES.txt' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/CNVkit-0.9.5.egg-info Skipping SOURCES.txt running install_scripts creating /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/snpfilter.sh -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_annotate -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_expression_correlate -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_updater -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_ztest -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-guess_baits -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-reference2targets -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-skg_convert -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_ztest to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit to 755 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.5 cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.5 --help-option='-h' \ ./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \ > ../debian/cnvkit-reference2targets.1; cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-0.9.5' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.5-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../cnvkit_0.9.5-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/1105190 and its subdirectories I: Current time: Mon Jan 2 13:05:19 -12 2023 I: pbuilder-time-stamp: 1672707919