I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 15 02:04:54 +14 2022 I: pbuilder-time-stamp: 1660478694 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_0.9.8-1.dsc] I: copying [./cnvkit_0.9.8.orig.tar.gz] I: copying [./cnvkit_0.9.8-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.NGblp2Uz/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 2 07:26:36 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.8-1.dsc dpkg-source: info: extracting cnvkit in cnvkit-0.9.8 dpkg-source: info: unpacking cnvkit_0.9.8.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.8-1.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7371/tmp/hooks/D01_modify_environment starting debug: Running on codethink13-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/7371/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/7371/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=7371 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.BqLV9DTE4B/pbuilderrc_ZqgW --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.BqLV9DTE4B/b2 --logfile b2/build.log --extrapackages usrmerge cnvkit_0.9.8-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 2021 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 2021 more -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount -rwxr-xr-x 1 root root 14496 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 15 02:05 sh -> bash lrwxrwxrwx 1 root root 4 Aug 14 05:48 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 2021 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 2021 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/7371/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-pyfaidx, help2man, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pyvcf, python3-future, python3-pomegranate, 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 ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-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 python3-pomegranate; however: Package python3-pomegranate 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} bsdextrautils{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} libbrotli1{a} libbsd0{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdebhelper-perl{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} libharfbuzz0b{a} libhts3{a} libice6{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{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} libpoppler102{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libsub-override-perl{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} libyaml-0-2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} poppler-utils{a} procps{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-joblib{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-networkx{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pomegranate{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pysam{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-tz{a} python3-vcf{a} python3-yaml{a} python3.9{a} python3.9-minimal{a} r-base-core{a} r-bioc-biocgenerics{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 libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx ncbi-blast+ poppler-data psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-gdal python3-html5lib python3-jinja2 python3-lxml python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygraphviz python3-pytest python3-renderpm python3-simplejson python3-tables python3-tk python3-xlwt r-base-dev r-cran-runit r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 162 newly installed, 0 to remove and 0 not upgraded. Need to get 108 MB of archives. After unpacking 381 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 mailcap all 3.69 [31.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 mime-support all 3.66 [10.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 fontconfig arm64 2.13.1-4.2 [416 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 fonts-lyx all 2.3.6-1 [205 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 help2man arm64 1.48.1 [190 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3 [101 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libpixman-1-0 arm64 0.40.0-1 [444 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.1-1 [310 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 libxcb-render0 arm64 1.14-3 [111 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libcairo2 arm64 1.16.0-5 [648 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+b1 [321 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 libdatrie1 arm64 0.2.13-1 [42.1 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 libfribidi0 arm64 1.0.8-2 [64.8 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 x11-common all 1:7.7+22 [252 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libimagequant0 arm64 2.12.2-1.1 [30.3 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 liblbfgsb0 arm64 3.0+dfsg.3-9 [24.5 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 liblcms2-2 arm64 2.12~rc1-2 [140 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 libnspr4 arm64 2:4.29-1 [105 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 libnss3 arm64 2:3.61-1 [1210 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 libopenjp2-7 arm64 2.4.0-3 [160 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 libthai-data all 0.1.28-3 [170 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 libthai0 arm64 0.1.28-3 [53.0 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libpango-1.0-0 arm64 1.46.2-3 [183 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 libpangoft2-1.0-0 arm64 1.46.2-3 [59.4 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 libpangocairo-1.0-0 arm64 1.46.2-3 [48.6 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 libpaper1 arm64 1.1.28+b1 [21.4 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libpaper-utils arm64 1.1.28+b1 [18.3 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1 [244 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1 [276 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 libpoppler102 arm64 20.09.0-3.1 [1594 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 libtcl8.6 arm64 8.6.11+dfsg-1 [964 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 libxft2 arm64 2.3.2-2 [51.3 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 libtk8.6 arm64 8.6.11-2 [738 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 libwebpdemux2 arm64 0.6.1-2.1 [87.5 kB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 libwebpmux3 arm64 0.6.1-2.1 [96.7 kB] Get: 126 http://deb.debian.org/debian bullseye/main arm64 libxt6 arm64 1:1.2.0-1 [176 kB] Get: 127 http://deb.debian.org/debian bullseye/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get: 128 http://deb.debian.org/debian bullseye/main arm64 poppler-utils arm64 20.09.0-3.1 [175 kB] Get: 129 http://deb.debian.org/debian bullseye/main arm64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 130 http://deb.debian.org/debian bullseye/main arm64 python3-all arm64 3.9.2-3 [1056 B] Get: 131 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 132 http://deb.debian.org/debian bullseye/main arm64 python3-numpy arm64 1:1.19.5-1 [3196 kB] Get: 133 http://deb.debian.org/debian bullseye/main arm64 python3-reportlab-accel arm64 3.5.59-2 [38.6 kB] Get: 134 http://deb.debian.org/debian bullseye/main arm64 python3-pil arm64 8.1.2+dfsg-0.2 [428 kB] Get: 135 http://deb.debian.org/debian bullseye/main arm64 python3-reportlab all 3.5.59-2 [575 kB] Get: 136 http://deb.debian.org/debian bullseye/main arm64 python3-biopython arm64 1.78+dfsg-4 [1389 kB] Get: 137 http://deb.debian.org/debian bullseye/main arm64 python3-six all 1.16.0-1 [17.1 kB] Get: 138 http://deb.debian.org/debian bullseye/main arm64 python3-cycler all 0.10.0-3 [8084 B] Get: 139 http://deb.debian.org/debian bullseye/main arm64 python3-dateutil all 2.8.1-5 [81.7 kB] Get: 140 http://deb.debian.org/debian bullseye/main arm64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 141 http://deb.debian.org/debian bullseye/main arm64 python3-future all 0.18.2-5 [349 kB] Get: 142 http://deb.debian.org/debian bullseye/main arm64 python3-joblib all 0.17.0-4 [213 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 python3-kiwisolver arm64 1.3.1-1+b1 [51.6 kB] Get: 144 http://deb.debian.org/debian bullseye/main arm64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 145 http://deb.debian.org/debian bullseye/main arm64 python3-matplotlib arm64 3.3.4-1 [4109 kB] Get: 146 http://deb.debian.org/debian bullseye/main arm64 python3-networkx all 2.5+ds-2 [900 kB] Get: 147 http://deb.debian.org/debian bullseye/main arm64 python3-tz all 2021.1-1 [34.8 kB] Get: 148 http://deb.debian.org/debian bullseye/main arm64 python3-pandas-lib arm64 1.1.5+dfsg-2 [2914 kB] Get: 149 http://deb.debian.org/debian bullseye/main arm64 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 150 http://deb.debian.org/debian bullseye/main arm64 python3-scipy arm64 1.6.0-2 [11.6 MB] Get: 151 http://deb.debian.org/debian bullseye/main arm64 python3-yaml arm64 5.3.1-4 [118 kB] Get: 152 http://deb.debian.org/debian bullseye/main arm64 python3-pomegranate arm64 0.13.5-1 [2307 kB] Get: 153 http://deb.debian.org/debian bullseye/main arm64 python3-pyfaidx all 0.5.9.2-1 [26.4 kB] Get: 154 http://deb.debian.org/debian bullseye/main arm64 python3-pysam arm64 0.15.4+ds-3+b2 [1386 kB] Get: 155 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Get: 156 http://deb.debian.org/debian bullseye/main arm64 python3-vcf arm64 0.6.8+git20170215.476169c-7+b3 [40.4 kB] Get: 157 http://deb.debian.org/debian bullseye/main arm64 zip arm64 3.0-12 [228 kB] Get: 158 http://deb.debian.org/debian bullseye/main arm64 unzip arm64 6.0-26 [165 kB] Get: 159 http://deb.debian.org/debian bullseye/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 160 http://deb.debian.org/debian bullseye/main arm64 r-base-core arm64 4.0.4-1 [24.9 MB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 r-bioc-dnacopy arm64 1.64.0-1 [418 kB] Fetched 108 MB in 2s (50.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../6-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../7-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../8-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20528 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.69_all.deb ... Unpacking mailcap (3.69) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../4-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../6-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20973 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../001-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:arm64. Preparing to unpack .../002-libprocps8_2%3a3.3.17-5_arm64.deb ... Unpacking libprocps8:arm64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a3.3.17-5_arm64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_1.1.1k-1_arm64.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../008-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... 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Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.2-1) ... Setting up libglib2.0-0:arm64 (2.66.8-1) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.6-1) ... Setting up unzip (6.0-26) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libjbig0:arm64 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up zip (3.0-12) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.1-1) ... Setting up libnspr4:arm64 (2:4.29-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up libfribidi0:arm64 (1.0.8-2) ... Setting up libimagequant0:arm64 (2.12.2-1.1) ... Setting up libpng16-16:arm64 (1.6.37-3) ... Setting up libtcl8.6:arm64 (8.6.11+dfsg-1) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:arm64 (0.6.1-2.1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... 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Setting up liblapack3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:arm64 (1.14-3) ... Setting up libwebpdemux2:arm64 (0.6.1-2.1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Setting up libnss3:arm64 (2:3.61-1) ... Setting up libxcb-shm0:arm64 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up libthai0:arm64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:arm64 (7.74.0-1.3+b1) ... Setting up libx11-6:arm64 (2:1.7.1-1) ... Setting up libharfbuzz0b:arm64 (2.7.4-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.3-9) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:arm64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libhts3:arm64 (1.11-4) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:arm64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libxt6:arm64 (1:1.2.0-1) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.2-2) ... Setting up libtk8.6:arm64 (8.6.11-2) ... Setting up libpango-1.0-0:arm64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libcairo2:arm64 (1.16.0-5) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-1) ... Setting up python3-pil:arm64 (8.1.2+dfsg-0.2) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:arm64 (3.5.59-2) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-reportlab (3.5.59-2) ... Setting up libpoppler102:arm64 (20.09.0-3.1) ... Setting up python3-dateutil (2.8.1-5) ... Setting up poppler-utils (20.09.0-3.1) ... Setting up libpangoft2-1.0-0:arm64 (1.46.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up libpangocairo-1.0-0:arm64 (1.46.2-3) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-pyfaidx (0.5.9.2-1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-joblib (0.17.0-4) ... Setting up python3-all (3.9.2-3) ... Setting up python3-yaml (5.3.1-4) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-vcf (0.6.8+git20170215.476169c-7+b3) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-future (0.18.2-5) ... 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 (1.78+dfsg-4) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up r-bioc-biocgenerics (0.36.0-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-pomegranate (0.13.5-1) ... Setting up python3-pandas-lib:arm64 (1.1.5+dfsg-2) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up r-bioc-dnacopy (1.64.0-1) ... Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... 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... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (1194 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 32011 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/cnvkit-0.9.8/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cnvkit_0.9.8-1_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan cd test && /usr/bin/make clean || /bin/true make[2]: Map '/build/cnvkit-0.9.8/test' wordt binnengegaan # 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]: Map '/build/cnvkit-0.9.8/test' wordt verlaten if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.9' 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]: Map '/build/cnvkit-0.9.8' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan [ -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:232: /usr/bin/python3 setup.py build running build running build_py creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/commands.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/vary.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/target.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/rna.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reports.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reference.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/plots.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/params.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/importers.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/fix.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/export.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/core.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cluster.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/call.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/bintest.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/batch.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/access.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/_version.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subtract.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subdivide.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/merge.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/intersect.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/gary.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/combiners.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/chromsort.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/cnvkit -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-skg_convert -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-reference2targets -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-guess_baits -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-cnv_updater -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-cnv_annotate -> build/scripts-3.9 copying /build/cnvkit-0.9.8/scripts/snpfilter.sh -> build/scripts-3.9 changing mode of build/scripts-3.9/cnvkit from 644 to 755 changing mode of build/scripts-3.9/cnvkit-skg_convert from 644 to 755 changing mode of build/scripts-3.9/cnvkit-reference2targets from 644 to 755 changing mode of build/scripts-3.9/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.9/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]: Map '/build/cnvkit-0.9.8' wordt verlaten debian/rules override_dh_auto_test make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan cd test && /usr/bin/make -j8 make[2]: Map '/build/cnvkit-0.9.8/test' wordt binnengegaan python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.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/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t_8rd72h because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y4tcy6i6 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j79yoy2x because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xejays5m because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m8fmps4j because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-repoqk0o because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hhpfn1bt because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-z_2tzq0k because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Created directory build/ Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 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/ Wrote build/p2-9_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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9leeri_9 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-enbgvirw because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lw2n_40h because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j42nmp_7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-25umc398 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gts5n7hi because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 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=0.0191 x 0.532 = 0.0102) --> assuming female Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 338 (5.0858%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 " chr1:2435319-2436685 log2=-0.709 spread=0.503 ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 " chr1:120611883-120612051 log2=0.070 spread=0.050 NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 " chr1:156842391-156842479 log2=-0.398 spread=0.290 MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 " chr1:183481886-183481951 log2=-0.040 spread=0.119 CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 " chr1:243800859-243801066 log2=0.023 spread=0.063 MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 " chr2:25536716-25536891 log2=0.702 spread=0.033 MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 REL chr2:61108881-61109061 log2=1.026 spread=0.559 " chr2:61128072-61128256 log2=0.115 spread=0.173 " chr2:61145275-61145462 log2=0.014 spread=0.099 CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 " chr2:128095237-128095425 log2=0.215 spread=0.212 METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 " chr3:97160189-97160367 log2=-0.050 spread=0.191 ATR chr3:142254935-142255077 log2=0.024 spread=0.027 " chr3:142286854-142287031 log2=-0.076 spread=0.116 GAK chr4:896278-896357 log2=-1.505 spread=1.261 FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 " chr4:1803044-1803507 log2=-0.073 spread=0.117 " chr4:1808792-1809022 log2=0.252 spread=0.108 CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 " chr4:178514600-178514725 log2=-0.098 spread=0.096 TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 " chr5:1295312-1295381 log2=-0.690 spread=0.462 CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 " chr5:25519857-25520034 log2=-0.015 spread=0.095 RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 " chr5:38962338-38962525 log2=0.005 spread=0.019 " chr5:38966685-38966862 log2=0.006 spread=0.165 " chr5:38978620-38978763 log2=0.040 spread=0.030 " chr5:39074133-39074327 log2=-0.158 spread=0.139 CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 " chr5:51030131-51030313 log2=-0.034 spread=0.192 MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 " chr5:56168412-56168590 log2=0.479 spread=0.038 CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 " chr5:86637023-86637168 log2=0.054 spread=0.111 " chr5:86642414-86642592 log2=0.254 spread=0.162 " chr5:86648912-86649096 log2=0.092 spread=0.062 " chr5:86670598-86670778 log2=0.222 spread=0.198 MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 APC chr5:112101965-112102138 log2=0.104 spread=0.217 NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 " chr5:170837567-170837631 log2=0.085 spread=0.349 FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 " chr5:180046203-180046404 log2=-1.531 spread=0.722 " chr5:180076418-180076603 log2=-2.224 spread=1.416 TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 " chr6:31939599-31940313 log2=-19.582 spread=0.181 STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 " chr6:31946632-31946824 log2=-20.052 spread=0.088 " chr6:31947142-31947366 log2=-20.114 spread=0.066 " chr6:31948176-31948360 log2=-19.982 spread=0.149 " chr6:31948382-31948612 log2=-19.757 spread=0.165 " chr6:31948730-31949253 log2=-20.048 spread=0.014 NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 " chr6:32164046-32164227 log2=-19.755 spread=0.189 " chr6:32164652-32164888 log2=-19.984 spread=0.154 " chr6:32165021-32165403 log2=-19.625 spread=0.196 " chr6:32166163-32166545 log2=-20.043 spread=0.072 " chr6:32166648-32166962 log2=-3.514 spread=5.742 " chr6:32168554-32168821 log2=-19.601 spread=0.197 " chr6:32168844-32169306 log2=-19.683 spread=0.166 " chr6:32169801-32170391 log2=-19.405 spread=0.205 " chr6:32171492-32171691 log2=-20.095 spread=0.101 " chr6:32171861-32172198 log2=-3.141 spread=7.288 " chr6:32178478-32178749 log2=-19.927 spread=0.164 " chr6:32180197-32180441 log2=-10.902 spread=9.532 " chr6:32180544-32180722 log2=-19.675 spread=0.186 " chr6:32180857-32181062 log2=-19.562 spread=0.227 " chr6:32181411-32181646 log2=-19.966 spread=0.171 " chr6:32181832-32182066 log2=-19.961 spread=0.172 " chr6:32182948-32183194 log2=-19.935 spread=0.168 " chr6:32184667-32185079 log2=-19.923 spread=0.165 " chr6:32185720-32185919 log2=-19.707 spread=0.197 " chr6:32187317-32187601 log2=-19.765 spread=0.173 " chr6:32187871-32188094 log2=-19.660 spread=0.188 " chr6:32188127-32188451 log2=-19.622 spread=0.169 " chr6:32188481-32188693 log2=-19.902 spread=0.132 " chr6:32188704-32189133 log2=-19.501 spread=0.193 " chr6:32190258-32190616 log2=-19.570 spread=0.209 " chr6:32190724-32190908 log2=-19.540 spread=0.232 " chr6:32191570-32191668 log2=-19.773 spread=0.178 " chr6:32191676-32191753 log2=-19.374 spread=0.201 FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 " chr6:128316545-128316699 log2=-0.070 spread=0.050 MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 " chr6:157099442-157099991 log2=-0.846 spread=0.504 " chr6:157100042-157100634 log2=-1.570 spread=0.825 IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 " chr7:98491365-98491541 log2=0.209 spread=0.153 " chr7:98493314-98493496 log2=0.389 spread=0.207 SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 " chr7:128829048-128829358 log2=-0.474 spread=0.315 BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 " chr7:140484736-140484912 log2=0.081 spread=0.150 " chr7:140487956-140488430 log2=-0.089 spread=0.142 " chr7:140493336-140493442 log2=-0.340 spread=0.283 " chr7:140624315-140624540 log2=-0.497 spread=0.342 TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 WRN chr8:30925752-30925890 log2=0.120 spread=0.158 " chr8:30941153-30941335 log2=0.079 spread=0.294 " chr8:30942625-30942802 log2=0.044 spread=0.247 " chr8:30947918-30948092 log2=0.151 spread=0.124 " chr8:31000128-31000252 log2=-0.099 spread=0.098 " chr8:31001006-31001182 log2=-0.002 spread=0.062 GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 " chr8:37698557-37699898 log2=-0.612 spread=0.029 ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 " chr8:48845528-48845758 log2=0.056 spread=0.196 " chr8:48866846-48867043 log2=-0.067 spread=0.097 " chr8:48868369-48868526 log2=-0.239 spread=0.174 " chr8:48872485-48872722 log2=-0.636 spread=0.464 CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 " chr9:2101491-2101640 log2=0.244 spread=0.104 JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 " chr9:5067014-5067883 log2=0.146 spread=0.089 " chr9:5068184-5070306 log2=0.133 spread=0.092 " chr9:5076944-5077152 log2=0.046 spread=0.137 PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 " chr9:21986759-21986899 log2=0.058 spread=0.175 LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 " chr9:87425375-87425452 log2=0.494 spread=0.066 PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 " chr9:139250747-139251032 log2=-0.223 spread=0.273 " chr9:139252418-139252703 log2=-0.512 spread=0.264 NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 " chr9:139417262-139417677 log2=-0.173 spread=0.191 " chr9:139440110-139440287 log2=-1.257 spread=0.500 MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 CGH chr10:22505654-22505837 log2=0.072 spread=0.107 RET chr10:43572644-43572830 log2=-1.376 spread=1.092 " chr10:43600360-43600677 log2=-0.341 spread=0.222 PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 " chr10:89685254-89685374 log2=0.244 spread=0.259 TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 " chr10:93579008-93579121 log2=0.166 spread=0.220 SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 " chr10:112679716-112679934 log2=-0.008 spread=0.028 CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 " chr11:94170270-94170454 log2=0.095 spread=0.285 YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 ATM chr11:108153392-108153639 log2=0.113 spread=0.136 " chr11:108164020-108164234 log2=-0.056 spread=0.040 " chr11:108217986-108218135 log2=0.359 spread=0.277 MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 " chr12:25391004-25391186 log2=0.368 spread=0.128 DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 " chr12:51206782-51207287 log2=-0.012 spread=0.101 PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 " chr13:26970356-26970536 log2=0.137 spread=0.121 FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 " chr13:32903506-32903689 log2=0.019 spread=0.232 " chr13:32918645-32918823 log2=0.158 spread=0.114 " chr13:32920899-32921077 log2=0.014 spread=0.247 RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 " chr13:48919164-48919369 log2=0.025 spread=0.094 " chr13:48921877-48922044 log2=0.106 spread=0.147 " chr13:48923026-48923204 log2=0.360 spread=0.016 " chr13:48938965-48939147 log2=0.084 spread=0.356 " chr13:48941578-48941767 log2=0.238 spread=0.212 " chr13:48947486-48947665 log2=0.025 spread=0.126 " chr13:48954166-48954251 log2=0.061 spread=0.273 " chr13:49037815-49038005 log2=0.063 spread=0.062 " chr13:49047410-49047589 log2=0.053 spread=0.170 CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 " chr13:85527771-85527948 log2=0.007 spread=0.222 GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 " chr13:110438332-110438432 log2=-3.643 spread=2.325 CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 " chr14:20291466-20291612 log2=0.697 spread=0.248 NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 " chr14:36989195-36989373 log2=0.023 spread=0.162 SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 " chr14:50619741-50619923 log2=0.003 spread=0.272 " chr14:50697856-50698044 log2=0.277 spread=0.334 MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 " chr14:71275790-71275923 log2=-2.815 spread=1.938 TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 CGH chr15:20870700-20870881 log2=1.102 spread=0.611 " chr15:38544477-38545455 log2=-0.348 spread=0.179 SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 " chr15:41803968-41804185 log2=-2.202 spread=0.188 " chr15:41804261-41804494 log2=-0.402 spread=0.392 NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 " chr16:2611404-2611585 log2=-5.171 spread=1.963 " chr16:2611721-2611943 log2=-11.810 spread=9.172 " chr16:2615504-2615725 log2=-20.113 spread=0.007 " chr16:2616307-2616486 log2=-20.054 spread=0.072 " chr16:2631267-2631414 log2=-20.009 spread=0.061 " chr16:2631583-2631734 log2=-20.089 spread=0.090 " chr16:2633363-2633616 log2=-20.101 spread=0.089 CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 CGH chr16:31526705-31526886 log2=0.057 spread=0.074 CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 " chr16:50826460-50826650 log2=0.239 spread=0.204 CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 " chr16:60005694-60005857 log2=-0.366 spread=0.298 CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 " chr17:12011053-12011253 log2=0.028 spread=0.232 NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 " chr17:29496854-29497046 log2=0.226 spread=0.193 RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 " chr17:30519172-30519355 log2=0.163 spread=0.289 " chr17:30525911-30526093 log2=-0.157 spread=0.046 ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 " chr19:2210351-2210545 log2=-0.860 spread=0.261 " chr19:2226130-2227152 log2=-0.113 spread=0.120 GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 " chr19:15311544-15311749 log2=-1.887 spread=1.202 JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 " chr19:33792774-33793010 log2=-1.781 spread=0.127 " chr19:33793014-33793356 log2=-0.541 spread=0.385 CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 " chr19:45873698-45873881 log2=-0.522 spread=0.327 BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 " chr21:36265140-36265318 log2=0.042 spread=0.039 CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 " chr22:29115325-29115465 log2=0.055 spread=0.390 SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 " chrX:1317372-1317594 log2=-21.121 spread=0.049 " chrX:1321225-1321435 log2=-20.851 spread=0.196 " chrX:1325274-1325530 log2=-21.121 spread=0.011 " chrX:1327651-1327830 log2=-21.000 spread=0.029 " chrX:1331391-1331576 log2=-21.018 spread=0.052 KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 " chrX:123185143-123185290 log2=-1.018 spread=0.062 " chrX:123202378-123202544 log2=-0.959 spread=0.103 FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 " chrY:9008607-9008759 log2=-1.012 spread=0.097 " chrY:13131970-13132039 log2=-1.004 spread=0.074 " chrY:19506485-19506650 log2=-1.018 spread=0.034 " chrY:21033918-21034071 log2=-1.013 spread=0.057 " chrY:28463435-28463622 log2=-0.952 spread=0.039 " chrY:28514033-28514208 log2=-0.992 spread=0.026 Antitargets: 108 (0.8597%) 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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gd04rj04 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vbl22s4_ because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-owahxyly because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3j19q45q because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rku30zos because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0tughl5j because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_cc3udvx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_1 Processing target: p2-5_5 Processing target: p2-20_2 Keeping 6308 of 6646 bins Processing target: p2-20_4 Processing target: p2-9_2 Processing target: p2-20_5 Keeping 6308 of 6646 bins Correcting for GC bias... Keeping 6308 of 6646 bins Processing target: p2-20_3 Correcting for density bias... Keeping 6308 of 6646 bins Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for GC bias... Keeping 6308 of 6646 bins Correcting for density bias... Processing antitarget: p2-20_1 Correcting for density bias... Correcting for GC bias... Keeping 6308 of 6646 bins Processing antitarget: p2-20_4 Correcting for density bias... Correcting for GC bias... Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_2 Correcting for density bias... Correcting for GC bias... Processing antitarget: p2-5_5 Correcting for density bias... Processing antitarget: p2-20_5 Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins Processing antitarget: p2-20_3 Processing antitarget: p2-9_2 Correcting for GC bias... Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... Keeping 12455 of 12563 bins WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Targets are 1.43 x more variable than antitargets Correcting for GC bias... Targets are 1.09 x more variable than antitargets WARNING: Skipping correction for RepeatMasker bias Targets are 1.14 x more variable than antitargets Targets are 1.14 x more variable than antitargets Targets are 2.60 x more variable than antitargets Antitargets are 1.08 x more variable than targets Wrote build/p2-20_4.cnr with 18763 regions Wrote build/p2-20_2.cnr with 18763 regions Wrote build/p2-5_5.cnr with 18763 regions Wrote build/p2-20_1.cnr with 18763 regions Targets are 1.75 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 Wrote build/p2-20_5.cnr with 18763 regions Wrote build/p2-20_3.cnr with 18763 regions 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 Wrote build/p2-9_2.cnr with 18763 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 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 segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fo7w6crx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3yt7f2jx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qo9jmoqb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-pxf023wa because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2ayj0s_7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-oeqzeiwz because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dad80ups because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0spj7140 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. 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 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-20_1 as female Treating sample p2-20_2 as female Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-5_5 as female Dropped 8 / 49 bins on chromosome chrY Dropped 7 / 49 bins on chromosome chrY Wrote build/p2-5_5.cns with 71 regions Dropped 6 / 49 bins on chromosome chrY python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf Wrote build/p2-20_2.cns with 125 regions Wrote build/p2-20_1.cns with 117 regions python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf Dropped 6 / 49 bins on chromosome chrY Dropped 8 / 49 bins on chromosome chrY Matplotlib created a temporary config/cache directory at /tmp/matplotlib-l6wo9pz4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_5.cns with 129 regions Wrote build/p2-20_4.cns with 137 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qj8edilu because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ufakglzb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. 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 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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-i8uz40ad because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fmwksayw because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Treating sample p2-20_2 as female Treating sample p2-5_5 as female Wrote p2-20_2-cbs-diagram.pdf Wrote p2-5_5-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 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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yslaxg5d because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Treating sample p2-20_1 as female Matplotlib created a temporary config/cache directory at /tmp/matplotlib-f81y1u9e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female Wrote p2-20_2-diagram.pdf Wrote p2-20_1-diagram.pdf 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 Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Matplotlib created a temporary config/cache directory at /tmp/matplotlib-utu9fzna because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yhmfqi68 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-u7cv6ar1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Selected test sample NA12882 and control sample NA12878 Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Wrote p2-9_2.nexus python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-w0van9cv because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 71 regions python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns Wrote p2-20_1-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 Wrote p2-all.cdt Wrote p2-5_5-both-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tvsrbsc_ because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. 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 call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-193yjdq4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1_hr99pb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rbea6weu because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_1 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 117 regions 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 Wrote p2-20_2-both-diagram.pdf Treating sample p2-20_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 125 regions python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 137 regions Wrote build/p2-20_5.call.cns with 129 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-n7tr3cyq because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zrnx7_99 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p0i3_oga because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9otzfqzc because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tph49am5 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-5_5-segmetrics.cns with 71 regions python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Wrote p2-5_5-metrics.tsv Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vyv1oi04 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-all-jtv.txt Wrote p2-9_2-diagram.pdf Placed 705 variants into 18763 bins Wrote p2-9_2.nexus-ogt Treating sample p2-20_1 as female Wrote p2-20_1-cbs-diagram.pdf Dropped 1 / 949 bins on chromosome chr6 Wrote p2-5_5-scatter.pdf Dropped 27 / 49 bins on chromosome chrY Dropped 11 / 49 bins on chromosome chrY Wrote build/p2-9_2.cns with 107 regions Wrote build/p2-20_3.cns with 74 regions 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 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 python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 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 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 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 python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-88955wuo because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-n9wph9_3 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7tsp3jod because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-r2iuuhm5 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3pne14yi because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4f9ilx3e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yvf7ed99 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ng8qgt2e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Detected file format: bed Showing 330 probes and 13 selected genes in region chr9:149999-45000000 Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 Showing 179 probes and 2 selected genes in region chr9:0-14504268 Showing 201 probes and 0 selected genes in region chr21 Treating sample p2-9_2 as female Showing 1480 probes and 0 selected genes in region chr1 Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 Wrote p2-9_2-cbs-diagram.pdf Wrote p2-9_2-chr21-scatter.pdf Wrote p2-9_2-SMARCA2-PTPRD-scatter.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 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 python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 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 Smoothing overshot at 3 / 97 indices: (-19.887157566382907, -3.337830278732162) vs. original (-19.2826, -0.27873000000000003) Wrote p2-9_2-chr1-scatter.pdf python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-alo31xv1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8vc1baab because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9q4ywfui because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zo6v9pfn because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-mvn26m3e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-sjfogrr6 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Treating sample p2-9_2 as female Treating sample p2-20_1 as female Treating sample p2-20_2 as female Treating sample p2-20_3 as female Treating sample p2-9_2 as female Treating sample p2-20_4 as female Treating sample p2-20_5 as female Found 15 gene breakpoints Wrote p2-9_2-breaks.txt python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns Treating sample p2-9_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 107 regions Wrote p2-all.seg Wrote gender-picard.txt 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 --t-test \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem --smooth-bootstrap python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Matplotlib created a temporary config/cache directory at /tmp/matplotlib-b46ixv7s because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-9_2-scatter.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zlxxjh15 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. 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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-s0umx3wu because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-f7yqmcni because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Found 53 gene-level gains and losses Wrote p2-9_2-genemetrics.txt Treating sample p2-20_3 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 74 regions which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr21-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 /usr/bin/pdfunite Matplotlib created a temporary config/cache directory at /tmp/matplotlib-in6hd_y7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. 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 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 Wrote p2-9_2.theta2.input Wrote heatmap-picard.pdf Matplotlib is building the font cache; this may take a moment. Wrote p2-9_2-metrics.tsv Matplotlib created a temporary config/cache directory at /tmp/matplotlib-invg7ufq because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-g3bjlzge because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-9_2-segmetrics.cns with 107 regions Treating sample p2-5_5.call as female Treating sample p2-9_2.call as female Treating sample p2-20_1.call as female Treating sample p2-9_2.call as female Treating sample p2-20_2.call as female Treating sample p2-20_3.call as female Treating sample p2-20_4.call as female Treating sample p2-20_5.call as female Wrote p2-all.bed Wrote p2-9_2.vcf Wrote p2-20-metrics.tsv Wrote p2-9_2-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]: Map '/build/cnvkit-0.9.8/test' wordt verlaten cd test && /usr/bin/make -j8 clean || /bin/true make[2]: Map '/build/cnvkit-0.9.8/test' wordt binnengegaan # 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]: Map '/build/cnvkit-0.9.8/test' wordt verlaten rm -Rf test/build test/*.tsv make[1]: Map '/build/cnvkit-0.9.8' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan [ -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:232: /usr/bin/python3 setup.py install --root /build/cnvkit-0.9.8/debian/cnvkit running install running build running build_py running build_scripts running install_lib creating /build/cnvkit-0.9.8/debian/cnvkit/usr creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9 creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/bedio.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/genepred.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/gff.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/picard.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seg.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/tab.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/util.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/chromsort.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/combiners.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/gary.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/intersect.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/merge.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/rangelabel.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subdivide.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subtract.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/none.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/_version.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/access.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/antitarget.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/autobin.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/batch.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/bintest.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/call.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cluster.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cmdutil.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cnary.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/core.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/coverage.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/descriptives.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/diagram.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/export.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/fix.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/heatmap.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/import_rna.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/importers.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/metrics.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/parallel.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/params.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/plots.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reference.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reports.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/rna.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/samutil.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/scatter.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segfilters.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmetrics.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/smoothing.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/target.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/vary.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/commands.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/gff.py to gff.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/picard.py to picard.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seg.py to seg.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/tab.py to tab.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/util.py to util.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/chromsort.py to chromsort.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/combiners.py to combiners.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/gary.py to gary.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/intersect.py to intersect.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/merge.py to merge.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subdivide.py to subdivide.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subtract.py to subtract.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/none.py to none.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/_version.py to _version.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/access.py to access.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/antitarget.py to antitarget.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/autobin.py to autobin.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/batch.py to batch.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/bintest.py to bintest.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/call.py to call.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cluster.py to cluster.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cnary.py to cnary.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/core.py to core.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/coverage.py to coverage.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/descriptives.py to descriptives.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/diagram.py to diagram.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/export.py to export.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/fix.py to fix.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/heatmap.py to heatmap.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/import_rna.py to import_rna.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/importers.py to importers.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/metrics.py to metrics.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/parallel.py to parallel.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/params.py to params.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/plots.py to plots.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reference.py to reference.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reports.py to reports.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/rna.py to rna.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/samutil.py to samutil.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/scatter.py to scatter.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segfilters.py to segfilters.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/smoothing.py to smoothing.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/target.py to target.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/vary.py to vary.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/commands.py to commands.cpython-39.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-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/CNVkit-0.9.8.egg-info Skipping SOURCES.txt running install_scripts creating /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/snpfilter.sh -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_annotate -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_expression_correlate -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_updater -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-guess_baits -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-reference2targets -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-skg_convert -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/snpfilter.sh to 775 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 changing mode of /build/cnvkit-0.9.8/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 0.9.8 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dv2fcb3m because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.8 --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]: Map '/build/cnvkit-0.9.8' wordt verlaten 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_installsystemduser -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_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -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: pakket 'cnvkit' wordt gebouwd in '../cnvkit_0.9.8-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../cnvkit_0.9.8-1_arm64.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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/7371/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/7371/tmp/hooks/B01_cleanup finished 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/7371 and its subdirectories I: Current time: Mon Aug 15 02:20:10 +14 2022 I: pbuilder-time-stamp: 1660479610