Diff of the two buildlogs: -- --- b1/build.log 2023-01-06 00:31:00.645163109 +0000 +++ b2/build.log 2023-01-06 00:34:42.997746268 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 5 12:25:44 -12 2023 -I: pbuilder-time-stamp: 1672964744 +I: Current time: Thu Feb 8 20:54:04 +14 2024 +I: pbuilder-time-stamp: 1707375244 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ 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.6NAPyt_z/trustedkeys.kbx': General error -gpgv: Signature made Fri Jan 1 05:26:36 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.1anwxQF_/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 @@ -32,135 +32,170 @@ dpkg-source: info: applying controldir I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/931345/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3964608/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +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' +lrwxrwxrwx 1 root root 4 Feb 8 20:54 /bin/sh -> 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/3964608/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3964608/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b46cc588656b4c1f9495d375de649039' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='931345' - PS1='# ' - PS2='> ' + INVOCATION_ID=d27f042889014368bf239a35997c4e36 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=3964608 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/pbuilderrc_RaDQ --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/b1 --logfile b1/build.log cnvkit_0.9.8-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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/r-b-build.S84apGfa/pbuilderrc_7V6U --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/b2 --logfile b2/build.log cnvkit_0.9.8-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.0.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.0.12-1~bpo11+1 (2022-12-19) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 20 21:25 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/931345/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jan 21 2022 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Feb 8 20:54 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 24 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3964608/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -390,7 +425,7 @@ Get: 160 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 r-bioc-dnacopy amd64 1.64.0-1 [420 kB] -Fetched 112 MB in 2s (50.9 MB/s) +Fetched 112 MB in 1s (85.2 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 ... 19704 files and directories currently installed.) @@ -1077,7 +1112,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/cnvkit-0.9.8/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cnvkit_0.9.8-1_source.changes +I: user script /srv/workspace/pbuilder/3964608/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3964608/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +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 @@ -1215,7 +1254,7 @@ make[1]: Leaving directory '/build/cnvkit-0.9.8' debian/rules override_dh_auto_test make[1]: Entering directory '/build/cnvkit-0.9.8' -cd test && /usr/bin/make -j15 +cd test && /usr/bin/make -j16 make[2]: Entering directory '/build/cnvkit-0.9.8/test' 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/ @@ -1232,54 +1271,54 @@ python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv -d build/ -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7hakm8jq because the default path (/nonexistent/first-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-xo2baud8 because the default path (/nonexistent/first-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-yld6gnn8 because the default path (/nonexistent/first-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-3wjczax3 because the default path (/nonexistent/first-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-xh2kp01l because the default path (/nonexistent/first-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-sogxkrpk because the default path (/nonexistent/first-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-wldtprjl because the default path (/nonexistent/first-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-sre15q01 because the default path (/nonexistent/first-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-p0wy30tt because the default path (/nonexistent/first-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-t4ewxr8b because the default path (/nonexistent/first-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-p38ce6g5 because the default path (/nonexistent/first-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-lw0zp9kq because the default path (/nonexistent/first-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-29_b75a8 because the default path (/nonexistent/first-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-xlshlwu1 because the default path (/nonexistent/first-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-njj2w36e because the default path (/nonexistent/first-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-6khogzap 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-zha92hit 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-3d86ovh5 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-ikl6fla8 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-ipw0vtxu 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-pwkjx6vl 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-_gcpb02_ 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-0k__go26 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-ew7abre9 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-neg6qh9t 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-n4b6s679 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-xu4a2hxs 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-f3fqvhl3 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-18eslir_ 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-qzdh0grh 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/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-20_2.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 Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -Wrote build/p2-20_5.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 -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_3.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions -Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_5.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 +Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 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 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-d_x1od88 because the default path (/nonexistent/first-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-jj8d0bgl 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. 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 @@ -1653,225 +1692,268 @@ 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-mrnsmr8c because the default path (/nonexistent/first-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-1k8fcway because the default path (/nonexistent/first-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-9sgeljs5 because the default path (/nonexistent/first-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-b2ob5k4_ because the default path (/nonexistent/first-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-zo6o8prv because the default path (/nonexistent/first-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-fl4_13kb because the default path (/nonexistent/first-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-w8u0g781 because the default path (/nonexistent/first-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_5 -Processing target: p2-20_3 -Keeping 6308 of 6646 bins -Processing target: p2-20_4 -Processing target: p2-5_5 -Correcting for GC bias... -Correcting for density bias... -Keeping 6308 of 6646 bins +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gzwnuh3r 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-wd640w42 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-a_njg7yt 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-9spce1vn 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-dwo84fk5 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-r9aeqouw 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-a70af87c 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: p2-9_2 +Processing target: p2-20_1 Keeping 6308 of 6646 bins -Processing antitarget: p2-20_5 Keeping 6308 of 6646 bins Correcting for GC bias... -Correcting for density bias... -Correcting for GC bias... Correcting for GC bias... Correcting for density bias... -Processing antitarget: p2-20_4 -Keeping 6308 of 6646 bins Correcting for density bias... +Processing antitarget: p2-9_2 +Processing antitarget: p2-20_1 +Processing target: p2-5_5 +Keeping 6308 of 6646 bins +Keeping 12455 of 12563 bins +Processing target: p2-20_2 +Processing target: p2-20_3 +Processing target: p2-20_5 +Processing target: p2-20_4 Keeping 12455 of 12563 bins -Processing antitarget: p2-5_5 Correcting for GC bias... -Processing antitarget: p2-20_3 Correcting for GC bias... -Correcting for density bias... -Keeping 12455 of 12563 bins -WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... -Processing antitarget: p2-9_2 -Keeping 12455 of 12563 bins +Correcting for density bias... WARNING: Skipping correction for RepeatMasker bias -Processing target: p2-20_1 -Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias -Keeping 12455 of 12563 bins -Keeping 12455 of 12563 bins -Processing target: p2-20_2 Keeping 6308 of 6646 bins -Targets are 2.60 x more variable than antitargets -Targets are 1.43 x more variable than antitargets +Keeping 6308 of 6646 bins +Keeping 6308 of 6646 bins +Keeping 6308 of 6646 bins +Processing antitarget: p2-5_5 Correcting for GC bias... Correcting for GC bias... -WARNING: Skipping correction for RepeatMasker bias -WARNING: Skipping correction for RepeatMasker bias -Keeping 6308 of 6646 bins Correcting for GC bias... -Correcting for density bias... Correcting for GC bias... Correcting for density bias... +Correcting for density bias... +Correcting for density bias... +Correcting for density bias... +Processing antitarget: p2-20_3 Targets are 1.75 x more variable than antitargets -Processing antitarget: p2-20_1 +Processing antitarget: p2-20_5 Processing antitarget: p2-20_2 -Wrote build/p2-20_5.cnr with 18763 regions -Wrote build/p2-20_4.cnr with 18763 regions +Keeping 12455 of 12563 bins +Processing antitarget: p2-20_4 Targets are 1.14 x more variable than antitargets +Correcting for GC bias... +WARNING: Skipping correction for RepeatMasker bias +Keeping 12455 of 12563 bins +Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins -Antitargets are 1.08 x more variable than targets -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns Correcting for GC bias... -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns +Keeping 12455 of 12563 bins +Correcting for GC bias... +Correcting for GC bias... Wrote build/p2-9_2.cnr with 18763 regions WARNING: Skipping correction for RepeatMasker bias -Keeping 12455 of 12563 bins +WARNING: Skipping correction for RepeatMasker bias +WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... +Wrote build/p2-20_1.cnr with 18763 regions +Targets are 1.14 x more variable than antitargets +WARNING: Skipping correction for RepeatMasker bias python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus -Targets are 1.14 x more variable than antitargets python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt +Targets are 2.60 x more variable than antitargets +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns +python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf +Targets are 1.09 x more variable than antitargets +Antitargets are 1.08 x more variable than targets Wrote build/p2-5_5.cnr with 18763 regions -WARNING: Skipping correction for RepeatMasker bias +Targets are 1.43 x more variable than antitargets +Wrote build/p2-20_5.cnr with 18763 regions +Wrote build/p2-20_2.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_3.cnr -o build/p2-20_3.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf -Targets are 1.09 x more variable than antitargets -Wrote build/p2-20_1.cnr with 18763 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0j66q4mu because the default path (/nonexistent/first-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_1.cnr -o build/p2-20_1.cns -python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nyqnl59v because the default path (/nonexistent/first-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_2.cnr with 18763 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-naka41bj because the default path (/nonexistent/first-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-08a_uaa1 because the default path (/nonexistent/first-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-cztr82rx because the default path (/nonexistent/first-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-5zrcrwtv because the default path (/nonexistent/first-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_2.cnr -o build/p2-20_2.cns python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns +Wrote build/p2-20_4.cnr with 18763 regions +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8n64j2lm 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-4zoyr4ph 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_4.cnr -o build/p2-20_4.cns python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ribrwm35 because the default path (/nonexistent/first-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-oreu0r__ because the default path (/nonexistent/first-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-19xn4v6l because the default path (/nonexistent/first-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-wdvm4jxz because the default path (/nonexistent/first-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-86vu7tmp because the default path (/nonexistent/first-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 -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rswfken2 because the default path (/nonexistent/first-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-enu9iynd because the default path (/nonexistent/first-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-2wdznea8 because the default path (/nonexistent/first-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-sa2h2j2g because the default path (/nonexistent/first-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 +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zw7j423t 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-x8v7sqn3 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-1ggn6ij4 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-ewqi76op 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-j6c0u4k1 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-enksvjzg 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-2cp328d7 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-c7s_itvf 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-k75j8fia 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-px0sc506 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-85sr4fgc 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-1ze9h05c 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-0w93nyg6 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 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes -Segmenting with method 'cbs', significance threshold 0.01, in 2 processes +Treating sample p2-9_2 as female Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records +Treating sample p2-20_1 as female +Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-5_5 as female 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 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Wrote p2-9_2.nexus -Treating sample p2-20_2 as female Dropped 1 / 949 bins on chromosome chr6 Placed 705 variants into 18763 bins Wrote p2-9_2.nexus-ogt Wrote p2-all.cdt Wrote p2-all-jtv.txt -Dropped 11 / 49 bins on chromosome chrY Dropped 27 / 49 bins on chromosome chrY -Dropped 8 / 49 bins on chromosome chrY -Dropped 8 / 49 bins on chromosome chrY -Dropped 7 / 49 bins on chromosome chrY -Wrote build/p2-20_3.cns with 74 regions -Wrote build/p2-9_2.cns with 107 regions -Wrote build/p2-5_5.cns with 71 regions -Wrote build/p2-20_4.cns with 137 regions -python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns +Wrote p2-5_5-diagram.pdf +Wrote p2-9_2-diagram.pdf Dropped 6 / 49 bins on chromosome chrY +Wrote p2-20_2-diagram.pdf +Wrote build/p2-9_2.cns with 107 regions +Dropped 11 / 49 bins on chromosome chrY 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 -Dropped 6 / 49 bins on chromosome chrY 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/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf -Wrote build/p2-20_2.cns with 125 regions python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf -Wrote build/p2-20_5.cns with 129 regions +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 +python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt Wrote build/p2-20_1.cns with 117 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bu52qg0q because the default path (/nonexistent/first-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-o9e58u0k because the default path (/nonexistent/first-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/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7kt3ch28 because the default path (/nonexistent/first-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-q7x7j13w because the default path (/nonexistent/first-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-8gb0ybeg because the default path (/nonexistent/first-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-u6fsxt7v because the default path (/nonexistent/first-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 -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wxdls6pt because the default path (/nonexistent/first-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-owo102de because the default path (/nonexistent/first-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. +Dropped 8 / 49 bins on chromosome chrY +Wrote build/p2-20_3.cns with 74 regions Wrote p2-20_1-diagram.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-51u239xp because the default path (/nonexistent/first-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/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf -Treating sample p2-20_3 as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2cboedyj because the default path (/nonexistent/first-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. -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-20_3.call.cns with 74 regions -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-mkwqgi11 because the default path (/nonexistent/first-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 -Wrote p2-5_5-cbs-diagram.pdf -Showing 1480 probes and 0 selected genes in region chr1 -Wrote p2-20_2-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 -Showing 201 probes and 0 selected genes in region chr21 +python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt +Dropped 6 / 49 bins on chromosome chrY +Dropped 7 / 49 bins on chromosome chrY +python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns +python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4n07ctwo 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. +Dropped 8 / 49 bins on chromosome chrY +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5laneo0j 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-175nyi0y 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-_5f9_m27 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-6p6kqzfg 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-q3p3sxkh 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-7obo132t 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-23oz4buk 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-v5_kcsm7 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/p2-5_5.cns with 71 regions +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ir1fi1y8 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_2.cns with 125 regions +python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns +Wrote build/p2-20_5.cns with 129 regions +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-253iw_a9 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-42a9fqik 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_4.cns with 137 regions +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 segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ + --ci -b 50 -a 0.5 Showing 330 probes and 13 selected genes in region chr9:149999-45000000 -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-diagram.pdf -Showing 179 probes and 2 selected genes in region chr9:0-14504268 -Wrote p2-5_5-diagram.pdf +Showing 201 probes and 0 selected genes in region chr21 Detected file format: bed Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 Treating sample p2-9_2 as female -Treating sample p2-20_2 as female -python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xej88al_ because the default path (/nonexistent/first-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 genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt -Wrote p2-9_2-chr21-scatter.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2_cc6kjl because the default path (/nonexistent/first-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-tysczoog because the default path (/nonexistent/first-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 p2-20_2-cbs-diagram.pdf +Showing 1480 probes and 0 selected genes in region chr1 +Treating sample p2-9_2 as female +Showing 179 probes and 2 selected genes in region chr9:0-14504268 +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bfbbxcl7 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. Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 Wrote p2-9_2-cbs-diagram.pdf +Found 15 gene breakpoints +Wrote p2-9_2-breaks.txt +Wrote p2-9_2-chr21-scatter.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lnx8620e 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-jtbk9q62 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-4lxql1cg 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-chr9p-scatter.pdf +python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv +python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv +Treating sample p2-9_2 as female +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 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 Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf +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 +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 +python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf +Smoothing overshot at 3 / 97 indices: (-19.887157566382854, -3.337830278732133) vs. original (-19.2826, -0.27873000000000003) Wrote p2-9_2-chr1-scatter.pdf -Wrote p2-9_2-chr9p-scatter.pdf +python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf +python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf +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-adbmqq7p 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_3 as female +Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-20_3.call.cns with 74 regions +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y9drhkoi 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-2j2h2uk2 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-75ijelps 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/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0a_um9lm 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-m_w9r7yb 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-htn2yrg5 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-5xz2hh4n 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-ibqcbfx2 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 +Wrote p2-9_2.theta2.input +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 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 +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vn_tf7gw 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 +Wrote p2-5_5-metrics.tsv +Wrote p2-9_2-metrics.tsv +Treating sample p2-20_1 as female +Wrote p2-5_5-cbs-diagram.pdf +Found 53 gene-level gains and losses +Wrote p2-9_2-genemetrics.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 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-2lei0lcy because the default path (/nonexistent/first-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/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns -python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns -python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns -Smoothing overshot at 3 / 97 indices: (-19.887157566382854, -3.337830278732133) vs. original (-19.2826, -0.27873000000000003) +Treating sample p2-20_2 as female +Wrote p2-20_1-cbs-diagram.pdf Treating sample p2-5_5 as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-413g5bt0 because the default path (/nonexistent/first-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_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p1_eei78 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 +Wrote p2-20_2-cbs-diagram.pdf python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-afm11ryd because the default path (/nonexistent/first-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-4rqwnagf because the default path (/nonexistent/first-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-nq_ewa9k because the default path (/nonexistent/first-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-2bf9jvk2 because the default path (/nonexistent/first-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-pg5fcjc0 because the default path (/nonexistent/first-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_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-6hyduupl 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 +Wrote p2-9_2-scatter.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rba6t7s6 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 p2-20_2 as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ibdn3kvl because the default path (/nonexistent/first-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-e6lj8_i4 because the default path (/nonexistent/first-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_1 as female -Treating sample p2-9_2 as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qjq53cgv because the default path (/nonexistent/first-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-up3z7dfv 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 p2-20-metrics.tsv +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t26l5c8v 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-h0qgx65d 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-1zywg72g 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-3y_gxst_ 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 @@ -1879,65 +1961,28 @@ Treating sample p2-20_3 as female Treating sample p2-20_4 as female Treating sample p2-20_5 as female -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 -python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns -Wrote p2-all.seg -python3 ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf -Treating sample p2-20_1 as female -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-20_1.call.cns with 117 regions -Found 15 gene breakpoints -Wrote p2-9_2-breaks.txt -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 Treating sample p2-5_5 as female Rescaling sample with purity 0.65, ploidy 2 -python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input Wrote build/p2-5_5.call.cns with 71 regions -Wrote gender-picard.txt -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 segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ - --ci -b 50 -a 0.5 -python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 137 regions -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-amhxsm8d because the default path (/nonexistent/first-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-43iv2nn5 because the default path (/nonexistent/first-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 -Wrote p2-9_2-scatter.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qnf0h1wn because the default path (/nonexistent/first-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-nkhi4qea because the default path (/nonexistent/first-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-qp9f5dni because the default path (/nonexistent/first-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-h5z_lrvp because the default path (/nonexistent/first-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 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-edrh53dr because the default path (/nonexistent/first-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 +Wrote p2-all.seg +Wrote gender-picard.txt +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 Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_5.call.cns with 129 regions -Treating sample p2-9_2.call as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hgbfyo6h because the default path (/nonexistent/first-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 heatmap-picard.pdf -python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-i3yc3gv5 because the default path (/nonexistent/first-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 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 +Treating sample p2-9_2.call as female Wrote p2-9_2.vcf -Wrote p2-5_5-metrics.tsv -Wrote p2-5_5-segmetrics.cns with 71 regions -Wrote p2-9_2-metrics.tsv -Wrote p2-9_2.theta2.input -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9ec_x21b because the default path (/nonexistent/first-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-31_6f4nm because the default path (/nonexistent/first-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 p2-20-metrics.tsv +Wrote p2-5_5-scatter.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t9xrq0lc 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. +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 +Wrote heatmap-picard.pdf Treating sample p2-5_5.call as female Treating sample p2-9_2.call as female Treating sample p2-20_1.call as female @@ -1946,20 +1991,14 @@ Treating sample p2-20_4.call as female Treating sample p2-20_5.call as female Wrote p2-all.bed -Treating sample p2-20_1 as female -Wrote p2-20_1-cbs-diagram.pdf -Wrote p2-9_2-segmetrics.cns with 107 regions -Wrote p2-5_5-scatter.pdf -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 -Wrote p2-5_5-both-diagram.pdf Wrote p2-9_2-both-diagram.pdf +Wrote p2-5_5-both-diagram.pdf Wrote p2-20_2-both-diagram.pdf Wrote p2-20_1-both-diagram.pdf which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf /usr/bin/pdfunite make[2]: Leaving directory '/build/cnvkit-0.9.8/test' -cd test && /usr/bin/make -j15 clean || /bin/true +cd test && /usr/bin/make -j16 clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.8/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf @@ -2138,7 +2177,7 @@ 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 755 +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 @@ -2150,7 +2189,7 @@ --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-ep60tkta because the default path (/nonexistent/first-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-1gu6siph 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.' \ @@ -2188,12 +2227,14 @@ 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/3964608/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3964608/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/931345 and its subdirectories -I: Current time: Thu Jan 5 12:31:00 -12 2023 -I: pbuilder-time-stamp: 1672965060 +I: removing directory /srv/workspace/pbuilder/3964608 and its subdirectories +I: Current time: Thu Feb 8 20:57:44 +14 2024 +I: pbuilder-time-stamp: 1707375464