Diff of the two buildlogs: -- --- b1/build.log 2021-07-12 05:41:42.775679470 +0000 +++ b2/build.log 2021-07-12 05:57:11.476863299 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jul 11 17:30:48 -12 2021 -I: pbuilder-time-stamp: 1626067848 +I: Current time: Mon Aug 15 02:04:54 +14 2022 +I: pbuilder-time-stamp: 1660478694 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ 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.S1qMA9wr/trustedkeys.kbx': General error -gpgv: Signature made Fri Jan 1 05:26:36 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.NGblp2Uz/trustedkeys.kbx': General error +gpgv: Signature made Sat Jan 2 07:26:36 2021 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.8-1.dsc @@ -31,135 +31,169 @@ dpkg-source: info: applying controldir I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/774/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/7371/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/7371/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/7371/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='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='774' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=7371 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.BqLV9DTE4B/pbuilderrc_MtR6 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.BqLV9DTE4B/b1 --logfile b1/build.log cnvkit_0.9.8-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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/tmp.BqLV9DTE4B/pbuilderrc_ZqgW --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.BqLV9DTE4B/b2 --logfile b2/build.log --extrapackages usrmerge cnvkit_0.9.8-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Feb 7 02:38 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Feb 7 02:38 more - -rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 9 21:25 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Feb 7 02:38 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/774/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Jun 22 2021 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Feb 8 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Feb 8 2021 more + -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount + -rwxr-xr-x 1 root root 14496 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 15 02:05 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 14 05:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Feb 8 2021 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Feb 8 2021 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/7371/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -389,7 +423,7 @@ Get: 160 http://deb.debian.org/debian bullseye/main arm64 r-base-core arm64 4.0.4-1 [24.9 MB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 r-bioc-dnacopy arm64 1.64.0-1 [418 kB] -Fetched 108 MB in 5s (22.2 MB/s) +Fetched 108 MB in 2s (50.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) @@ -1075,8 +1109,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1194 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 32011 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -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 +hostname: Temporary failure in name resolution +I: Running cd /build/cnvkit-0.9.8/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cnvkit_0.9.8-1_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.8-1 dpkg-buildpackage: info: source distribution unstable @@ -1086,12 +1157,12 @@ debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan cd test && /usr/bin/make clean || /bin/true -make[2]: Entering directory '/build/cnvkit-0.9.8/test' +make[2]: Map '/build/cnvkit-0.9.8/test' wordt binnengegaan # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf -make[2]: Leaving directory '/build/cnvkit-0.9.8/test' +make[2]: Map '/build/cnvkit-0.9.8/test' wordt verlaten if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:232: python3.9 setup.py clean @@ -1101,7 +1172,7 @@ 'build/scripts-3.9' does not exist -- can't clean it rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info -make[1]: Leaving directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -1112,7 +1183,7 @@ I: pybuild base:232: python3.9 setup.py config running config debian/rules override_dh_auto_build -make[1]: Entering directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ @@ -1211,11 +1282,11 @@ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py -make[1]: Leaving directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan cd test && /usr/bin/make -j8 -make[2]: Entering directory '/build/cnvkit-0.9.8/test' +make[2]: Map '/build/cnvkit-0.9.8/test' wordt binnengegaan python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.antitargetcoverage.csv -d build/ @@ -1224,58 +1295,59 @@ python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tmzlu_5y 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-0kpkhjwu 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-64f21e4_ 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-v47c8wa2 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-eawy5cur 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-s_u6l1dk 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-map71d61 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-h09clvaj 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-t_8rd72h because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y4tcy6i6 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j79yoy2x because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xejays5m because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m8fmps4j because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-repoqk0o because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hhpfn1bt because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-z_2tzq0k because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Created directory build/ -Wrote build/p2-20_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/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions -Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ +Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ -Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions +python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions -WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions -python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ -python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn -python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ -WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions +python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hi9kx3hq 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-wr_c5ttk 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-st07vn73 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-3j8ei6ux 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-5790r_yi 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-zmcqy4le 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/p2-9_5.antitargetcoverage.cnn with 12563 regions +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9leeri_9 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-enbgvirw because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lw2n_40h because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j42nmp_7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-25umc398 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gts5n7hi because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions +WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions Number of target and antitarget files: 3, 3 No FASTA reference genome provided; skipping GC, RM calculations -WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female -Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female -Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions -WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female -Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female @@ -1283,7 +1355,6 @@ Correcting for GC bias... Correcting for density bias... Loading build/p2-5_5.targetcoverage.cnn -Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions Correcting for GC bias... Correcting for density bias... Loading build/p2-9_5.targetcoverage.cnn @@ -1645,324 +1716,325 @@ 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-t6s5jg7w 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-ivpe7b0g 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-4jcwsrcz 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-3gqzy0au 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-qu4kn1qc 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-fp5yc7dy 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-n0fb__v3 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: p2-9_2 -Processing target: p2-20_5 -Processing target: p2-20_2 +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gd04rj04 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vbl22s4_ because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-owahxyly because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3j19q45q because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rku30zos because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0tughl5j because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_cc3udvx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Processing target: p2-20_1 Processing target: p2-5_5 -Keeping 6308 of 6646 bins +Processing target: p2-20_2 Keeping 6308 of 6646 bins Processing target: p2-20_4 -Processing target: p2-20_1 -Correcting for GC bias... +Processing target: p2-9_2 +Processing target: p2-20_5 Keeping 6308 of 6646 bins -Correcting for density bias... -Processing target: p2-20_3 Correcting for GC bias... Keeping 6308 of 6646 bins +Processing target: p2-20_3 Correcting for density bias... Keeping 6308 of 6646 bins Keeping 6308 of 6646 bins -Processing antitarget: p2-9_2 +Correcting for GC bias... Correcting for GC bias... Keeping 6308 of 6646 bins +Correcting for density bias... +Processing antitarget: p2-20_1 +Correcting for density bias... Correcting for GC bias... +Keeping 6308 of 6646 bins +Processing antitarget: p2-20_4 +Correcting for density bias... Correcting for GC bias... Correcting for GC bias... -Processing antitarget: p2-20_5 -Correcting for density bias... -Correcting for density bias... Correcting for density bias... +Processing antitarget: p2-20_2 Correcting for density bias... Correcting for GC bias... -Correcting for density bias... -Processing antitarget: p2-20_1 Processing antitarget: p2-5_5 -Processing antitarget: p2-20_4 -Processing antitarget: p2-20_2 +Correcting for density bias... +Processing antitarget: p2-20_5 Keeping 12455 of 12563 bins -Processing antitarget: p2-20_3 Keeping 12455 of 12563 bins +Processing antitarget: p2-20_3 +Processing antitarget: p2-9_2 Correcting for GC bias... Keeping 12455 of 12563 bins -WARNING: Skipping correction for RepeatMasker bias -Keeping 12455 of 12563 bins -Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... Keeping 12455 of 12563 bins -WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins WARNING: Skipping correction for RepeatMasker bias +WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins Correcting for GC bias... Correcting for GC bias... -Targets are 1.75 x more variable than antitargets +WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... +Keeping 12455 of 12563 bins WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias +Targets are 1.43 x more variable than antitargets +Correcting for GC bias... +Targets are 1.09 x more variable than antitargets WARNING: Skipping correction for RepeatMasker bias -Targets are 2.60 x more variable than antitargets -Wrote build/p2-9_2.cnr with 18763 regions Targets are 1.14 x more variable than antitargets -Targets are 1.09 x more variable than antitargets Targets are 1.14 x more variable than antitargets +Targets are 2.60 x more variable than antitargets Antitargets are 1.08 x more variable than targets -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 -Targets are 1.43 x more variable than antitargets -Wrote build/p2-20_5.cnr with 18763 regions +Wrote build/p2-20_4.cnr with 18763 regions Wrote build/p2-20_2.cnr with 18763 regions -Wrote build/p2-20_1.cnr with 18763 regions Wrote build/p2-5_5.cnr with 18763 regions -python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus +Wrote build/p2-20_1.cnr with 18763 regions +Targets are 1.75 x more variable than antitargets +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns +Wrote build/p2-20_5.cnr with 18763 regions Wrote build/p2-20_3.cnr with 18763 regions -python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt -Wrote build/p2-20_4.cnr with 18763 regions -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 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 segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-57udigww 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-x5a7tveh 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-ulnjdt8_ 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-m0c0onky 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-xhk5_vrf 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-0t5rrkbw 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-jtsivx9_ 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-kv_dl_jd 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 +python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf +Wrote build/p2-9_2.cnr with 18763 regions +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns +python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns +python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fo7w6crx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3yt7f2jx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qo9jmoqb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-pxf023wa because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2ayj0s_7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-oeqzeiwz because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dad80ups because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0spj7140 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes -Treating sample p2-9_2 as female -Selected test sample NA12882 and control sample NA12878 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes -Wrote p2-9_2.nexus -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns -Loaded 3654 records; skipped: 514 somatic, 394 depth -Kept 2631 heterozygous of 3654 VCF records Segmenting with method 'cbs', significance threshold 0.01, in 2 processes -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wm26skfa 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 1 / 949 bins on chromosome chr6 +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 -Dropped 27 / 49 bins on chromosome chrY -Placed 705 variants into 18763 bins -Wrote p2-9_2.nexus-ogt +Treating sample p2-5_5 as female Dropped 8 / 49 bins on chromosome chrY -Wrote build/p2-9_2.cns with 107 regions -python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf -Dropped 6 / 49 bins on chromosome chrY -python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf +Dropped 7 / 49 bins on chromosome chrY Wrote build/p2-5_5.cns with 71 regions -python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf +Dropped 6 / 49 bins on chromosome chrY +python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf +Wrote build/p2-20_2.cns with 125 regions Wrote build/p2-20_1.cns with 117 regions -Dropped 7 / 49 bins on chromosome chrY -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-jg34o5u8 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 -o p2-5_5-cbs-diagram.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-asir2ri7 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_2.cns with 125 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-58x0rpg6 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 -o p2-9_2-cbs-diagram.pdf -Wrote build/p2-20_4.cns with 137 regions -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-jvmat51a 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 p2-20_1 as female -Treating sample p2-5_5 as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-n7qxd962 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 p2-20_2 as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7wuldlae 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 Dropped 6 / 49 bins on chromosome chrY -Treating sample p2-5_5 as female +Dropped 8 / 49 bins on chromosome chrY +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-l6wo9pz4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_5.cns with 129 regions -Wrote p2-5_5-cbs-diagram.pdf -Treating sample p2-9_2 as female -python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf +Wrote build/p2-20_4.cns with 137 regions +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qj8edilu because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ufakglzb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf -Wrote p2-9_2-cbs-diagram.pdf -Treating sample p2-20_1 as female -Wrote p2-20_1-cbs-diagram.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y2ynoe3a 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 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-y66y4z8c 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-w03j5f3_ 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-kecfzjqe 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 +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-i8uz40ad because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fmwksayw because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Treating sample p2-9_2 as female Treating sample p2-20_2 as female -Wrote p2-9_2-diagram.pdf +Treating sample p2-5_5 as female Wrote p2-20_2-cbs-diagram.pdf +Wrote p2-5_5-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf -python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt +python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yslaxg5d because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Treating sample p2-5_5 as female Treating sample p2-20_1 as female -Treating sample p2-9_2 as female -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-6gkz5uff 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-9gz569uf 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-f81y1u9e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female -Found 15 gene breakpoints -Wrote p2-9_2-breaks.txt -python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9_yp64ir 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 -Found 53 gene-level gains and losses -Wrote p2-9_2-genemetrics.txt -Wrote p2-5_5-both-diagram.pdf -python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt -python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-mos_cz0u 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-dd2tsrpj 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 gender-picard.txt -Wrote p2-20_1-both-diagram.pdf +Wrote p2-20_2-diagram.pdf +Wrote p2-20_1-diagram.pdf python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt +python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus +Wrote p2-5_5-diagram.pdf +python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-utu9fzna because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yhmfqi68 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-u7cv6ar1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Selected test sample NA12882 and control sample NA12878 +Loaded 3654 records; skipped: 514 somatic, 394 depth +Kept 2631 heterozygous of 3654 VCF records +Wrote p2-9_2.nexus python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns -Wrote p2-20_1-diagram.pdf -Wrote p2-9_2-both-diagram.pdf -python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-w0van9cv because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Treating sample p2-5_5 as female +Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-5_5.call.cns with 71 regions python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wmres6bt 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-diagram.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zqlo7ae5 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-3y90agf0 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 p2-5_5-diagram.pdf +Wrote p2-20_1-both-diagram.pdf python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cszems2j 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-all.cdt +Wrote p2-5_5-both-diagram.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tvsrbsc_ because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns -Wrote p2-20_2-both-diagram.pdf python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns -Treating sample p2-9_2 as female -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-9_2.call.cns with 107 regions -Treating sample p2-5_5 as female -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-5_5.call.cns with 71 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-o5_a2kvp 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-o0iya1am 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 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 +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-193yjdq4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1_hr99pb because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rbea6weu because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_1 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 117 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-uspfuzb8 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 segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ --ci -b 50 -a 0.5 +Wrote p2-20_2-both-diagram.pdf Treating sample p2-20_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 125 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-uzrto6hm 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-1intnxq7 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-kd98o5r5 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/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-20_4.call.cns with 137 regions Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-20_4.call.cns with 137 regions Wrote build/p2-20_5.call.cns with 129 regions -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-n7tr3cyq because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2jczfu29 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-6n_0m1_1 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-y060xuef 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 p2-9_2.theta2.input -Wrote p2-5_5-segmetrics.cns with 71 regions 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 -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 +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zrnx7_99 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p0i3_oga because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9otzfqzc because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tph49am5 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Wrote p2-5_5-segmetrics.cns with 71 regions +python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf +Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Wrote p2-5_5-metrics.tsv -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 -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yzq5nx6_ 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-p077d84z 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 p2-9_2-metrics.tsv -Wrote p2-9_2-segmetrics.cns with 107 regions -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-o__cgpwo 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-vyv1oi04 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Wrote p2-all-jtv.txt +Wrote p2-9_2-diagram.pdf +Placed 705 variants into 18763 bins +Wrote p2-9_2.nexus-ogt +Treating sample p2-20_1 as female +Wrote p2-20_1-cbs-diagram.pdf +Dropped 1 / 949 bins on chromosome chr6 +Wrote p2-5_5-scatter.pdf +Dropped 27 / 49 bins on chromosome chrY +Dropped 11 / 49 bins on chromosome chrY +Wrote build/p2-9_2.cns with 107 regions +Wrote build/p2-20_3.cns with 74 regions +python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf +python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wxikgnan 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-cflgg_q1 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. -Showing 1480 probes and 0 selected genes in region chr1 -Wrote p2-all.cdt 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 -Showing 201 probes and 0 selected genes in region chr21 -Wrote p2-9_2-chr1-scatter.pdf -Showing 330 probes and 13 selected genes in region chr9:149999-45000000 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 -Smoothing overshot at 3 / 97 indices: (-19.887157566382907, -3.337830278732162) vs. original (-19.2826, -0.27873000000000003) -Wrote p2-9_2-chr21-scatter.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gp4_tp00 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. -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 -Wrote p2-9_2-chr9p-scatter.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-27j02p92 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 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 -Showing 179 probes and 2 selected genes in region chr9:0-14504268 -Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k9hybp2x 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 -o p2-9_2-cbs-diagram.pdf +python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-88955wuo because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-n9wph9_3 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7tsp3jod because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-r2iuuhm5 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3pne14yi because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4f9ilx3e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yvf7ed99 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ng8qgt2e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Treating sample p2-9_2 as female Detected file format: bed +Showing 330 probes and 13 selected genes in region chr9:149999-45000000 Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 +Showing 179 probes and 2 selected genes in region chr9:0-14504268 +Showing 201 probes and 0 selected genes in region chr21 +Treating sample p2-9_2 as female +Showing 1480 probes and 0 selected genes in region chr1 Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 -Wrote p2-5_5-scatter.pdf -Treating sample p2-9_2.call as female -Wrote p2-9_2.vcf -Wrote p2-all-jtv.txt -Wrote p2-9_2-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 -Dropped 11 / 49 bins on chromosome chrY -Wrote build/p2-20_3.cns with 74 regions +Wrote p2-9_2-cbs-diagram.pdf +Wrote p2-9_2-chr21-scatter.pdf +Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf python3 ../cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf +Wrote p2-9_2-chr9p-scatter.pdf +python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt +python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt +python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt python3 ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg -python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns -python3 ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t1i6oqlh 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-ok5ya3yp 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-h9zlzoqy 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-0z8pwmcn 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. +Smoothing overshot at 3 / 97 indices: (-19.887157566382907, -3.337830278732162) vs. original (-19.2826, -0.27873000000000003) +Wrote p2-9_2-chr1-scatter.pdf +python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-alo31xv1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8vc1baab because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9q4ywfui because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zo6v9pfn because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-mvn26m3e because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-sjfogrr6 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Treating sample p2-9_2 as female Treating sample p2-20_1 as female -Wrote p2-all.seg -Treating sample p2-20_3 as female -Rescaling sample with purity 0.65, ploidy 2 Treating sample p2-20_2 as female -Wrote build/p2-20_3.call.cns with 74 regions Treating sample p2-20_3 as female +Treating sample p2-9_2 as female Treating sample p2-20_4 as female Treating sample p2-20_5 as female +Found 15 gene breakpoints +Wrote p2-9_2-breaks.txt +python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns +Treating sample p2-9_2 as female +Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-9_2.call.cns with 107 regions +Wrote p2-all.seg +Wrote gender-picard.txt +python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input +python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ + --mean --median --mode --t-test \ + --stdev --mad --mse --iqr --bivar \ + --ci --pi --sem --smooth-bootstrap +python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-b46ixv7s because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Wrote p2-9_2-scatter.pdf +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zlxxjh15 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +python3 ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-s0umx3wu because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-f7yqmcni because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Found 53 gene-level gains and losses +Wrote p2-9_2-genemetrics.txt +Treating sample p2-20_3 as female +Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-20_3.call.cns with 74 regions +which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr21-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf +/usr/bin/pdfunite +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-in6hd_y7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +python3 ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf python3 ../cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed -Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9mcg7mfp 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 p2-9_2.theta2.input +Wrote heatmap-picard.pdf +Matplotlib is building the font cache; this may take a moment. +Wrote p2-9_2-metrics.tsv +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-invg7ufq because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Matplotlib created a temporary config/cache directory at /tmp/matplotlib-g3bjlzge because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +Wrote p2-9_2-segmetrics.cns with 107 regions Treating sample p2-5_5.call as female Treating sample p2-9_2.call as female Treating sample p2-20_1.call as female +Treating sample p2-9_2.call as female Treating sample p2-20_2.call as female Treating sample p2-20_3.call as female Treating sample p2-20_4.call as female Treating sample p2-20_5.call as female Wrote p2-all.bed -Wrote heatmap-picard.pdf -make[2]: Leaving directory '/build/cnvkit-0.9.8/test' +Wrote p2-9_2.vcf +Wrote p2-20-metrics.tsv +Wrote p2-9_2-both-diagram.pdf +which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf +/usr/bin/pdfunite +make[2]: Map '/build/cnvkit-0.9.8/test' wordt verlaten cd test && /usr/bin/make -j8 clean || /bin/true -make[2]: Entering directory '/build/cnvkit-0.9.8/test' +make[2]: Map '/build/cnvkit-0.9.8/test' wordt binnengegaan # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf -make[2]: Leaving directory '/build/cnvkit-0.9.8/test' +make[2]: Map '/build/cnvkit-0.9.8/test' wordt verlaten rm -Rf test/build test/*.tsv -make[1]: Leaving directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install -make[1]: Entering directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt binnengegaan [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ @@ -2130,7 +2202,7 @@ 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 @@ -2142,7 +2214,7 @@ --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-yeewjnlx 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-dv2fcb3m because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.8 --help-option='-h' \ ./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \ @@ -2151,7 +2223,7 @@ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py -make[1]: Leaving directory '/build/cnvkit-0.9.8' +make[1]: Map '/build/cnvkit-0.9.8' wordt verlaten dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild @@ -2172,7 +2244,7 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.8-1_arm64.deb'. +dpkg-deb: pakket 'cnvkit' wordt gebouwd in '../cnvkit_0.9.8-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../cnvkit_0.9.8-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2180,12 +2252,14 @@ 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/7371/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/7371/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/774 and its subdirectories -I: Current time: Sun Jul 11 17:41:40 -12 2021 -I: pbuilder-time-stamp: 1626068500 +I: removing directory /srv/workspace/pbuilder/7371 and its subdirectories +I: Current time: Mon Aug 15 02:20:10 +14 2022 +I: pbuilder-time-stamp: 1660479610