Diff of the two buildlogs: -- --- b1/build.log 2021-11-30 18:42:19.082914467 +0000 +++ b2/build.log 2021-11-30 18:48:24.670371551 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 2 13:00:34 -12 2023 -I: pbuilder-time-stamp: 1672707634 +I: Current time: Wed Dec 1 08:42:20 +14 2021 +I: pbuilder-time-stamp: 1638297740 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Wed Mar 27 22:43:40 2019 -12 +gpgv: Signature made Fri Mar 29 00:43:40 2019 +14 gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438 gpgv: issuer "osallou@debian.org" gpgv: Can't check signature: No public key @@ -32,136 +32,170 @@ dpkg-source: info: applying controldir I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1105190/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3397097/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +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/3397097/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3397097/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='2642de1da2c741bbabdb20b099dad18c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1105190' - PS1='# ' - PS2='> ' + INVOCATION_ID=22dc9bd75ffe4406b58a581fe9163d19 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3397097 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.RcEykp4YkN/pbuilderrc_ujLs --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RcEykp4YkN/b1 --logfile b1/build.log cnvkit_0.9.5-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.RcEykp4YkN/pbuilderrc_rfDO --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RcEykp4YkN/b2 --logfile b2/build.log cnvkit_0.9.5-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 10 16:21 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/1105190/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 1 08:42 sh -> bash + lrwxrwxrwx 1 root root 4 Nov 8 11:58 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/3397097/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -383,7 +417,7 @@ Get: 154 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get: 156 http://deb.debian.org/debian buster/main amd64 r-bioc-dnacopy amd64 1.56.0-1 [419 kB] -Fetched 103 MB in 2s (68.3 MB/s) +Fetched 103 MB in 2s (65.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) @@ -1052,7 +1086,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/cnvkit-0.9.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cnvkit_0.9.5-3_source.changes +hostname: Name or service not known +I: Running cd /build/cnvkit-0.9.5/ && 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_0.9.5-3_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.5-3 dpkg-buildpackage: info: source distribution unstable @@ -1176,14 +1211,14 @@ copying and adjusting ./scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_annotate -> build/scripts-3.7 copying ./scripts/snpfilter.sh -> build/scripts-3.7 -changing mode of build/scripts-3.7/cnvkit from 644 to 755 -changing mode of build/scripts-3.7/cnvkit-skg_convert from 644 to 755 -changing mode of build/scripts-3.7/cnvkit-reference2targets from 644 to 755 -changing mode of build/scripts-3.7/cnvkit-guess_baits from 644 to 755 -changing mode of build/scripts-3.7/cnvkit-cnv_ztest from 644 to 755 -changing mode of build/scripts-3.7/cnvkit-cnv_updater from 644 to 755 -changing mode of build/scripts-3.7/cnvkit-cnv_expression_correlate from 644 to 755 -changing mode of build/scripts-3.7/cnvkit-cnv_annotate from 644 to 755 +changing mode of build/scripts-3.7/cnvkit from 664 to 775 +changing mode of build/scripts-3.7/cnvkit-skg_convert from 664 to 775 +changing mode of build/scripts-3.7/cnvkit-reference2targets from 664 to 775 +changing mode of build/scripts-3.7/cnvkit-guess_baits from 664 to 775 +changing mode of build/scripts-3.7/cnvkit-cnv_ztest from 664 to 775 +changing mode of build/scripts-3.7/cnvkit-cnv_updater from 664 to 775 +changing mode of build/scripts-3.7/cnvkit-cnv_expression_correlate from 664 to 775 +changing mode of build/scripts-3.7/cnvkit-cnv_annotate from 664 to 775 cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done @@ -1191,7 +1226,7 @@ make[1]: Leaving directory '/build/cnvkit-0.9.5' debian/rules override_dh_auto_test make[1]: Entering directory '/build/cnvkit-0.9.5' -cd test && /usr/bin/make -j16 +cd test && /usr/bin/make -j15 make[2]: Entering directory '/build/cnvkit-0.9.5/test' python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-20_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ @@ -1209,29 +1244,29 @@ python3 ../cnvkit.py import-picard picard/p2-20_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Created directory build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' +Wrote build/p2-20_5.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/p2-9_2.targetcoverage.cnn with 6646 regions -Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions -Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions -Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions -Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions +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.targetcoverage.cnn with 6646 regions -Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions -Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions +Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' -Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions +Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions -Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions +Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions @@ -1366,105 +1401,105 @@ python3 ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr python3 ../cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr python3 ../cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr -Processing target: p2-20_5 Processing target: p2-20_3 +Processing target: p2-20_4 Keeping 6557 of 6646 bins -Processing target: p2-20_2 +Processing target: p2-5_5 Correcting for GC bias... +Keeping 6557 of 6646 bins Correcting for density bias... +Correcting for GC bias... +Processing target: p2-20_1 Keeping 6557 of 6646 bins +Correcting for density bias... +Processing target: p2-20_5 Correcting for GC bias... Correcting for density bias... +Processing target: p2-9_2 Keeping 6557 of 6646 bins -Processing target: p2-5_5 -Processing antitarget: p2-20_5 +Processing antitarget: p2-20_3 Correcting for GC bias... -Processing target: p2-20_4 -Processing antitarget: p2-20_2 -Keeping 12452 of 12563 bins -Keeping 6557 of 6646 bins +Processing antitarget: p2-20_4 Correcting for density bias... -Correcting for GC bias... +Keeping 6557 of 6646 bins +Keeping 6557 of 6646 bins +Processing antitarget: p2-5_5 Keeping 12452 of 12563 bins Correcting for GC bias... -Correcting for density bias... -WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... -Keeping 6557 of 6646 bins Correcting for GC bias... -Processing antitarget: p2-5_5 +Keeping 12452 of 12563 bins Correcting for density bias... -WARNING: Skipping correction for RepeatMasker bias -Targets are 1.60 x more variable than antitargets -Processing antitarget: p2-20_3 -Processing target: p2-9_2 -Processing target: p2-20_1 +Processing antitarget: p2-20_1 Keeping 12452 of 12563 bins -Processing antitarget: p2-20_4 +Correcting for density bias... +Correcting for GC bias... +WARNING: Skipping correction for RepeatMasker bias +Processing target: p2-20_2 Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Keeping 12452 of 12563 bins -Keeping 12452 of 12563 bins -Targets are 1.04 x more variable than antitargets -Keeping 6557 of 6646 bins -Keeping 6557 of 6646 bins +Processing antitarget: p2-20_5 +WARNING: Skipping correction for RepeatMasker bias +Processing antitarget: p2-9_2 Correcting for GC bias... -Wrote build/p2-20_5.cnr with 19009 regions +Keeping 6557 of 6646 bins +Antitargets are 1.01 x more variable than targets Correcting for GC bias... +Targets are 1.18 x more variable than antitargets +WARNING: Skipping correction for RepeatMasker bias Targets are 1.09 x more variable than antitargets +Correcting for density bias... +Keeping 12452 of 12563 bins +Keeping 12452 of 12563 bins Correcting for GC bias... Correcting for GC bias... -Correcting for density bias... WARNING: Skipping correction for RepeatMasker bias -Correcting for density bias... WARNING: Skipping correction for RepeatMasker bias -Processing antitarget: p2-20_1 -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns +Processing antitarget: p2-20_2 +Wrote build/p2-20_4.cnr with 19009 regions +Targets are 1.60 x more variable than antitargets +Wrote build/p2-20_3.cnr with 19009 regions +Targets are 1.08 x more variable than antitargets Wrote build/p2-5_5.cnr with 19009 regions -Antitargets are 1.01 x more variable than targets +Targets are 1.34 x more variable than antitargets Keeping 12452 of 12563 bins +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns Correcting for GC bias... -Targets are 1.18 x more variable than antitargets -Processing antitarget: p2-9_2 +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf -Wrote build/p2-20_2.cnr with 19009 regions -WARNING: Skipping correction for RepeatMasker bias -Wrote build/p2-20_3.cnr with 19009 regions -Targets are 1.08 x more variable than antitargets -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns -python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf -Keeping 12452 of 12563 bins -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns -Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias +Wrote build/p2-20_5.cnr with 19009 regions Wrote build/p2-20_1.cnr with 19009 regions -Wrote build/p2-20_4.cnr with 19009 regions +Wrote build/p2-9_2.cnr with 19009 regions +Targets are 1.04 x more variable than antitargets +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 segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf -Targets are 1.34 x more variable than antitargets -python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns -Segmenting with method 'cbs', significance threshold 0.01, in 2 processes -Wrote build/p2-9_2.cnr with 19009 regions -Segmenting with method 'cbs', significance threshold 0.01, in 2 processes -Segmenting with method 'cbs', significance threshold 0.01, in 2 processes python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf -python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt -python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt -Segmenting with method 'cbs', significance threshold 0.01, in 2 processes +Wrote build/p2-20_2.cnr with 19009 regions +python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns +python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf +python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt +python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt Treating sample p2-5_5 as male -Treating sample p2-20_2 as male -Treating sample p2-20_1 as male +Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Selected test sample NA12882 and control sample NA12878 -Treating sample p2-9_2 as male +Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Loaded 3654 records; skipped: 514 somatic, 394 depth +Treating sample p2-20_1 as male Kept 2631 heterozygous of 3654 VCF records +Segmenting with method 'cbs', significance threshold 0.01, in 2 processes +Treating sample p2-9_2 as male +Segmenting with method 'cbs', significance threshold 0.01, in 2 processes +Treating sample p2-20_2 as male Wrote p2-9_2.nexus /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] @@ -1571,8 +1606,6 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] -Wrote build/p2-20_5.cns with 64 regions -python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -1757,6 +1790,8 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] +Wrote build/p2-20_3.cns with 48 regions +Wrote build/p2-5_5.cns with 49 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -1801,16 +1836,12 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] +Dropped 1 / 5 bins on chromosome chrY +Wrote build/p2-20_1.cns with 78 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] -Wrote build/p2-20_2.cns with 77 regions -Wrote build/p2-5_5.cns with 49 regions -python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf -python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf -python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns -python3 ../cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -1855,8 +1886,6 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] -Wrote build/p2-20_3.cns with 48 regions -python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -1891,8 +1920,6 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] -Dropped 1 / 5 bins on chromosome chrY -Treating sample p2-20_2 as male /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -1903,6 +1930,9 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] +Wrote build/p2-20_4.cns with 65 regions +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 diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -1985,13 +2015,6 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] -Wrote build/p2-20_4.cns with 65 regions -Wrote p2-20_2-cbs-diagram.pdf -Treating sample p2-20_5 as male -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-20_5.call.cns with 64 regions -Treating sample p2-20_2 as male -python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -2002,6 +2025,10 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] +python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf +python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns +python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns +Wrote build/p2-20_5.cns with 64 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -2038,7 +2065,18 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] -python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns +Wrote build/p2-9_2.cns with 57 regions +python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns +python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns +Wrote p2-20_1-diagram.pdf +python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input +Treating sample p2-5_5 as male +Treating sample p2-20_3 as male +Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-20_3.call.cns with 48 regions +Treating sample p2-5_5 as male +Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-5_5.call.cns with 49 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. @@ -2131,104 +2169,102 @@ b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] -Wrote build/p2-9_2.cns with 57 regions -python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns -Treating sample p2-20_2 as male -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-20_2.call.cns with 77 regions -Wrote build/p2-20_1.cns with 78 regions -python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns -python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem -Treating sample p2-5_5 as male -Wrote p2-5_5-cbs-diagram.pdf -Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ --ci -b 50 -a 0.5 -python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv +Wrote build/p2-20_2.cns with 77 regions Treating sample p2-5_5 as male -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-5_5.call.cns with 49 regions -Treating sample p2-20_3 as male -Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-20_3.call.cns with 48 regions +Wrote p2-5_5-cbs-diagram.pdf +python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Treating sample p2-20_4 as male -python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Rescaling sample with purity 0.65, ploidy 2 -Treating sample p2-5_5 as male Wrote build/p2-20_4.call.cns with 65 regions +python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv python3 ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv +Wrote p2-9_2-diagram.pdf +Treating sample p2-20_5 as male +Rescaling sample with purity 0.65, ploidy 2 python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf +Wrote build/p2-20_5.call.cns with 64 regions +Placed 727 variants into 19009 bins +Wrote p2-9_2.nexus-ogt Wrote p2-20_2-diagram.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf -Wrote p2-9_2.theta2.input +Wrote p2-5_5-diagram.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 -Wrote p2-5_5-metrics.tsv python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf -Wrote p2-5_5-segmetrics.cns with 49 regions -Wrote p2-9_2-metrics.tsv python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf -Wrote p2-20_1-diagram.pdf +Wrote p2-9_2.theta2.input python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf -Wrote p2-9_2-segmetrics.cns with 57 regions +Wrote p2-5_5-segmetrics.cns with 49 regions +Wrote p2-9_2-metrics.tsv python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf +Showing 186 probes and 2 selected genes in region chr9:0-14504268 +python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf +Showing 1498 probes and 0 selected genes in region chr1 +Detected file format: bed +Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf +Showing 43 probes and 1 selected genes in region chr9:2000000-4000000 +Wrote p2-5_5-metrics.tsv +Wrote p2-20-metrics.tsv +Showing 54 probes and 1 selected genes in region chr9:8000000-12000000 +Showing 341 probes and 14 selected genes in region chr9:149999-45000000 python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf -/build/cnvkit-0.9.5/cnvlib/export.py:70: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. - ("GWEIGHT", 1), -Wrote p2-all.cdt -Wrote p2-9_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf +python3 ../cnvkit.py 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 heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf -Showing 1498 probes and 0 selected genes in region chr1 -Showing 341 probes and 14 selected genes in region chr9:149999-45000000 -Placed 727 variants into 19009 bins -Wrote p2-9_2.nexus-ogt -Showing 186 probes and 2 selected genes in region chr9:0-14504268 +Treating sample p2-9_2 as male +Wrote p2-9_2-segmetrics.cns with 57 regions +Wrote p2-9_2-cbs-diagram.pdf +Treating sample p2-20_1 as male +Wrote p2-20_1-cbs-diagram.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 -Treating sample p2-9_2 as male python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt -Wrote p2-all-jtv.txt -Wrote p2-20-metrics.tsv -Treating sample p2-20_1 as male -Wrote p2-9_2-cbs-diagram.pdf -Detected file format: bed -Showing 43 probes and 1 selected genes in region chr9:2000000-4000000 -Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf -Wrote p2-9_2-chr1-scatter.pdf +/build/cnvkit-0.9.5/cnvlib/export.py:70: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. + ("GWEIGHT", 1), +Wrote p2-all.cdt python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt python3 ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg -Wrote p2-20_1-cbs-diagram.pdf -Showing 54 probes and 1 selected genes in region chr9:8000000-12000000 -Wrote p2-5_5-scatter.pdf +Treating sample p2-20_2 as male python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns +Wrote p2-20_2-cbs-diagram.pdf python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns -Treating sample p2-9_2 as male +Wrote p2-9_2-chr1-scatter.pdf Treating sample p2-5_5 as male Treating sample p2-9_2 as male Treating sample p2-20_1 as male +python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Treating sample p2-20_2 as male Treating sample p2-20_3 as male Treating sample p2-20_4 as male Treating sample p2-20_5 as male +Wrote p2-all-jtv.txt +Wrote p2-5_5-scatter.pdf +Treating sample p2-20_2 as male +Treating sample p2-9_2 as male Treating sample p2-20_1 as male +Treating sample p2-20_1 as male +Rescaling sample with purity 0.65, ploidy 2 +Wrote build/p2-20_1.call.cns with 78 regions Found 1 gene breakpoints Wrote p2-9_2-breaks.txt Treating sample p2-9_2 as male +Wrote p2-all.seg +Treating sample p2-20_2 as male Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-9_2.call.cns with 57 regions -Treating sample p2-20_1 as male +Wrote build/p2-20_2.call.cns with 77 regions +Treating sample p2-9_2 as male Rescaling sample with purity 0.65, ploidy 2 -Wrote build/p2-20_1.call.cns with 78 regions -Wrote p2-all.seg +Wrote build/p2-9_2.call.cns with 57 regions python3 ../cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed python3 ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf -Treating sample p2-9_2 as male Wrote gender-picard.txt -Wrote p2-20_2-both-diagram.pdf +Wrote heatmap-picard.pdf +Wrote p2-5_5-both-diagram.pdf Treating sample p2-5_5.call as male Treating sample p2-9_2.call as male Treating sample p2-20_1.call as male @@ -2236,22 +2272,21 @@ Treating sample p2-20_3.call as male Treating sample p2-20_4.call as male Treating sample p2-20_5.call as male +Found 322 gene-level gains and losses +Wrote p2-9_2-genemetrics.txt Wrote p2-all.bed -Wrote heatmap-picard.pdf -Wrote p2-9_2-scatter.pdf Treating sample p2-9_2.call as male +Wrote p2-9_2.vcf +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-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf -Wrote p2-5_5-both-diagram.pdf /usr/bin/pdfunite -Wrote p2-9_2.vcf -Found 322 gene-level gains and losses -Wrote p2-9_2-genemetrics.txt Wrote p2-9_2-both-diagram.pdf +Wrote p2-20_2-both-diagram.pdf Wrote p2-20_1-both-diagram.pdf which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf /usr/bin/pdfunite make[2]: Leaving directory '/build/cnvkit-0.9.5/test' -cd test && /usr/bin/make -j16 clean || /bin/true +cd test && /usr/bin/make -j15 clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.5/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf @@ -2431,15 +2466,15 @@ copying build/scripts-3.7/cnvkit-reference2targets -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-skg_convert -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/snpfilter.sh to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_ztest to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 -changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit to 755 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/snpfilter.sh to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_ztest to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-guess_baits to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-reference2targets to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-skg_convert to 775 +changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit to 775 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 @@ -2480,12 +2515,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3397097/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3397097/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/1105190 and its subdirectories -I: Current time: Mon Jan 2 13:05:19 -12 2023 -I: pbuilder-time-stamp: 1672707919 +I: removing directory /srv/workspace/pbuilder/3397097 and its subdirectories +I: Current time: Wed Dec 1 08:48:24 +14 2021 +I: pbuilder-time-stamp: 1638298104