I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 12 19:32:25 +14 2021 I: pbuilder-time-stamp: 1626067945 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bio-tradis_1.4.5+dfsg2-1.dsc] I: copying [./bio-tradis_1.4.5+dfsg2.orig.tar.xz] I: copying [./bio-tradis_1.4.5+dfsg2-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.SMQsWjch/trustedkeys.kbx': General error gpgv: Signature made Sun Jan 12 05:56:13 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bio-tradis_1.4.5+dfsg2-1.dsc dpkg-source: info: extracting bio-tradis in bio-tradis-1.4.5+dfsg2 dpkg-source: info: unpacking bio-tradis_1.4.5+dfsg2.orig.tar.xz dpkg-source: info: unpacking bio-tradis_1.4.5+dfsg2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying samtools1.10 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/822/tmp/hooks/D01_modify_environment starting debug: Running on virt32b. 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/822/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/822/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=1bcfca15e2b545b29ba66d87dcc3d9fa LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=822 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.M48vRmf4U9/pbuilderrc_Xxr6 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.M48vRmf4U9/b2 --logfile b2/build.log --extrapackages usrmerge bio-tradis_1.4.5+dfsg2-1.dsc' SUDO_GID=112 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 5.10.0-7-armmp-lpae #1 SMP Debian 5.10.40-1 (2021-05-28) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 9636 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 26668 Sep 23 2020 cat -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash -rwxr-xr-x 1 root root 75880 Sep 23 2020 date -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd -rwxr-xr-x 1 root root 59912 Sep 23 2020 df -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir -rwxr-xr-x 1 root root 55012 Feb 8 04:38 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 22508 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 12 19:32 sh -> bash lrwxrwxrwx 1 root root 4 Jul 9 23:26 sh.distrib -> dash -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/822/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libbio-perl-perl, libenv-path-perl, libexception-class-perl, libmoose-perl, libtest-exception-perl, libtest-files-perl, libtest-most-perl, libtest-simple-perl, libtext-csv-perl, libtry-tiny-perl, perl, samtools, smalt, tabix, bwa dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libenv-path-perl; however: Package libenv-path-perl is not installed. pbuilder-satisfydepends-dummy depends on libexception-class-perl; however: Package libexception-class-perl is not installed. pbuilder-satisfydepends-dummy depends on libmoose-perl; however: Package libmoose-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-exception-perl; however: Package libtest-exception-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-files-perl; however: Package libtest-files-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libtext-csv-perl; however: Package libtext-csv-perl is not installed. pbuilder-satisfydepends-dummy depends on libtry-tiny-perl; however: Package libtry-tiny-perl is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on smalt; however: Package smalt is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} bwa{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libalgorithm-c3-perl{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libb-hooks-op-check-perl{a} libbambamc0{a} libbio-perl-perl{a} libbrotli1{a} libcapture-tiny-perl{a} libclass-c3-perl{a} libclass-data-inheritable-perl{a} libclass-load-perl{a} libclass-load-xs-perl{a} libcurl3-gnutls{a} libdata-optlist-perl{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-overloadinfo-perl{a} libdevel-stacktrace-perl{a} libdist-checkconflicts-perl{a} libdynaloader-functions-perl{a} libelf1{a} libenv-path-perl{a} libeval-closure-perl{a} libexception-class-perl{a} libfile-stripnondeterminism-perl{a} libhts3{a} libicu67{a} libio-string-perl{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmodule-implementation-perl{a} libmodule-runtime-conflicts-perl{a} libmodule-runtime-perl{a} libmoose-perl{a} libmro-compat-perl{a} libncurses6{a} libnghttp2-14{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libparams-classify-perl{a} libparams-util-perl{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-identify-perl{a} libsub-install-perl{a} libsub-name-perl{a} libsub-override-perl{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-files-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} samtools{a} sensible-utils{a} smalt{a} tabix{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run ca-certificates curl libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclass-c3-xs-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdevel-lexalias-perl libdevel-partialdump-perl libgd-perl libgpm2 libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtext-csv-xs-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk publicsuffix wget 0 packages upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 25.3 MB of archives. After unpacking 82.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-7 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf bwa armhf 0.7.17-6+b1 [197 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libalgorithm-c3-perl all 0.11-1 [11.7 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libb-hooks-op-check-perl armhf 0.22-1+b3 [11.0 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libbambamc0 armhf 0.0.50-4 [30.7 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libio-string-perl all 1.08-3.1 [11.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libdata-stag-perl all 0.14-2 [448 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libclass-c3-perl all 0.35-1 [22.9 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 44 http://deb.debian.org/debian bullseye/main armhf libparams-util-perl armhf 1.102-1+b1 [24.6 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libsub-install-perl all 0.928-1.1 [10.8 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libdata-optlist-perl all 0.110-1.1 [10.8 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libdevel-callchecker-perl armhf 0.008-1+b2 [15.7 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libparams-classify-perl armhf 0.015-1+b3 [24.5 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf libpackage-stash-perl all 0.39-1 [21.9 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libclass-load-perl all 0.25-1 [16.1 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf libclass-load-xs-perl armhf 0.10-1+b5 [14.2 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 65 http://deb.debian.org/debian bullseye/main armhf libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 66 http://deb.debian.org/debian bullseye/main armhf libdevel-globaldestruction-perl all 0.14-1.1 [8312 B] Get: 67 http://deb.debian.org/debian bullseye/main armhf libmro-compat-perl all 0.13-1 [12.2 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libsub-identify-perl armhf 0.14-1+b3 [11.6 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf libdevel-overloadinfo-perl all 0.005-1 [7212 B] Get: 70 http://deb.debian.org/debian bullseye/main armhf libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf libdist-checkconflicts-perl all 0.11-1.1 [10.2 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libenv-path-perl all 0.19-2 [19.5 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf libsub-exporter-perl all 0.987-1 [47.2 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf libeval-closure-perl all 0.14-1 [11.5 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf libexception-class-perl all 1.44-1 [32.3 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libmodule-runtime-conflicts-perl all 0.003-1.1 [7156 B] Get: 78 http://deb.debian.org/debian bullseye/main armhf libsub-name-perl armhf 0.26-1+b1 [13.2 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf libpackage-deprecationmanager-perl all 0.17-1.1 [16.6 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf libpackage-stash-xs-perl armhf 0.29-1+b2 [18.6 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf libmoose-perl armhf 2.2014-2 [802 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get: 84 http://deb.debian.org/debian bullseye/main armhf libtest-deep-perl all 1.130-1 [49.3 kB] Get: 85 http://deb.debian.org/debian bullseye/main armhf libtext-diff-perl all 1.45-1 [27.7 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libtest-differences-perl all 0.67-1 [18.7 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf libtest-exception-perl all 0.43-1 [18.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main armhf libtest-files-perl all 0.15-1 [12.0 kB] Get: 89 http://deb.debian.org/debian bullseye/main armhf libtest-warn-perl all 0.36-1 [16.2 kB] Get: 90 http://deb.debian.org/debian bullseye/main armhf libtest-most-perl all 0.37-1 [24.9 kB] Get: 91 http://deb.debian.org/debian bullseye/main armhf libtext-csv-perl all 2.00-1 [105 kB] Get: 92 http://deb.debian.org/debian bullseye/main armhf samtools armhf 1.11-1 [519 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf smalt armhf 0.7.6-9 [98.0 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf tabix armhf 1.11-4 [306 kB] Fetched 25.3 MB in 3s (9324 kB/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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_armhf.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bwa. Preparing to unpack .../16-bwa_0.7.17-6+b1_armhf.deb ... Unpacking bwa (0.7.17-6+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../24-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../26-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.7_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libalgorithm-c3-perl. Preparing to unpack .../32-libalgorithm-c3-perl_0.11-1_all.deb ... Unpacking libalgorithm-c3-perl (0.11-1) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../33-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../34-libb-hooks-op-check-perl_0.22-1+b3_armhf.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b3) ... Selecting previously unselected package libbambamc0. Preparing to unpack .../35-libbambamc0_0.0.50-4_armhf.deb ... Unpacking libbambamc0 (0.0.50-4) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../36-libio-string-perl_1.08-3.1_all.deb ... Unpacking libio-string-perl (1.08-3.1) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../37-libdata-stag-perl_0.14-2_all.deb ... Unpacking libdata-stag-perl (0.14-2) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../38-libbio-perl-perl_1.7.7-2_all.deb ... Unpacking libbio-perl-perl (1.7.7-2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../39-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../40-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libclass-c3-perl. Preparing to unpack .../41-libclass-c3-perl_0.35-1_all.deb ... Unpacking libclass-c3-perl (0.35-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../42-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../43-libparams-util-perl_1.102-1+b1_armhf.deb ... Unpacking libparams-util-perl (1.102-1+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../44-libsub-install-perl_0.928-1.1_all.deb ... Unpacking libsub-install-perl (0.928-1.1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../45-libdata-optlist-perl_0.110-1.1_all.deb ... Unpacking libdata-optlist-perl (0.110-1.1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../46-libdynaloader-functions-perl_0.003-1.1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1.1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../47-libdevel-callchecker-perl_0.008-1+b2_armhf.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b2) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../48-libparams-classify-perl_0.015-1+b3_armhf.deb ... Unpacking libparams-classify-perl (0.015-1+b3) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../49-libmodule-runtime-perl_0.016-1_all.deb ... Unpacking libmodule-runtime-perl (0.016-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../50-libtry-tiny-perl_0.30-1_all.deb ... Unpacking libtry-tiny-perl (0.30-1) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../51-libmodule-implementation-perl_0.09-1.1_all.deb ... Unpacking libmodule-implementation-perl (0.09-1.1) ... Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../52-libpackage-stash-perl_0.39-1_all.deb ... Unpacking libpackage-stash-perl (0.39-1) ... Selecting previously unselected package libclass-load-perl. Preparing to unpack .../53-libclass-load-perl_0.25-1_all.deb ... Unpacking libclass-load-perl (0.25-1) ... Selecting previously unselected package libclass-load-xs-perl. Preparing to unpack .../54-libclass-load-xs-perl_0.10-1+b5_armhf.deb ... Unpacking libclass-load-xs-perl (0.10-1+b5) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../55-libsasl2-modules-db_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../56-libsasl2-2_2.1.27+dfsg-2.1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:armhf. Preparing to unpack .../57-libldap-2.4-2_2.4.57+dfsg-3_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../58-libnghttp2-14_1.43.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.43.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../59-libpsl5_0.21.0-1.2_armhf.deb ... Unpacking libpsl5:armhf (0.21.0-1.2) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../60-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../61-libssh2-1_1.9.0-2_armhf.deb ... Unpacking libssh2-1:armhf (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../62-libcurl3-gnutls_7.74.0-1.3+b1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../63-libdeflate0_1.7-1_armhf.deb ... Unpacking libdeflate0:armhf (1.7-1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../64-libsub-exporter-progressive-perl_0.001013-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-1) ... Selecting previously unselected package libdevel-globaldestruction-perl. Preparing to unpack .../65-libdevel-globaldestruction-perl_0.14-1.1_all.deb ... Unpacking libdevel-globaldestruction-perl (0.14-1.1) ... Selecting previously unselected package libmro-compat-perl. Preparing to unpack .../66-libmro-compat-perl_0.13-1_all.deb ... Unpacking libmro-compat-perl (0.13-1) ... Selecting previously unselected package libsub-identify-perl. Preparing to unpack .../67-libsub-identify-perl_0.14-1+b3_armhf.deb ... Unpacking libsub-identify-perl (0.14-1+b3) ... Selecting previously unselected package libdevel-overloadinfo-perl. Preparing to unpack .../68-libdevel-overloadinfo-perl_0.005-1_all.deb ... Unpacking libdevel-overloadinfo-perl (0.005-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../69-libdevel-stacktrace-perl_2.0400-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libdist-checkconflicts-perl. Preparing to unpack .../70-libdist-checkconflicts-perl_0.11-1.1_all.deb ... Unpacking libdist-checkconflicts-perl (0.11-1.1) ... Selecting previously unselected package libenv-path-perl. Preparing to unpack .../71-libenv-path-perl_0.19-2_all.deb ... Unpacking libenv-path-perl (0.19-2) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../72-libsub-exporter-perl_0.987-1_all.deb ... Unpacking libsub-exporter-perl (0.987-1) ... Selecting previously unselected package libeval-closure-perl. Preparing to unpack .../73-libeval-closure-perl_0.14-1_all.deb ... Unpacking libeval-closure-perl (0.14-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../74-libexception-class-perl_1.44-1_all.deb ... Unpacking libexception-class-perl (1.44-1) ... Selecting previously unselected package libhts3:armhf. Preparing to unpack .../75-libhts3_1.11-4_armhf.deb ... Unpacking libhts3:armhf (1.11-4) ... Selecting previously unselected package libmodule-runtime-conflicts-perl. Preparing to unpack .../76-libmodule-runtime-conflicts-perl_0.003-1.1_all.deb ... Unpacking libmodule-runtime-conflicts-perl (0.003-1.1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../77-libsub-name-perl_0.26-1+b1_armhf.deb ... Unpacking libsub-name-perl (0.26-1+b1) ... Selecting previously unselected package libpackage-deprecationmanager-perl. Preparing to unpack .../78-libpackage-deprecationmanager-perl_0.17-1.1_all.deb ... Unpacking libpackage-deprecationmanager-perl (0.17-1.1) ... Selecting previously unselected package libpackage-stash-xs-perl. Preparing to unpack .../79-libpackage-stash-xs-perl_0.29-1+b2_armhf.deb ... Unpacking libpackage-stash-xs-perl (0.29-1+b2) ... Selecting previously unselected package libmoose-perl. Preparing to unpack .../80-libmoose-perl_2.2014-2_armhf.deb ... Unpacking libmoose-perl (2.2014-2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../81-libncurses6_6.2+20201114-2_armhf.deb ... Unpacking libncurses6:armhf (6.2+20201114-2) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../82-libsub-uplevel-perl_0.2800-1.1_all.deb ... Unpacking libsub-uplevel-perl (0.2800-1.1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../83-libtest-deep-perl_1.130-1_all.deb ... Unpacking libtest-deep-perl (1.130-1) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../84-libtext-diff-perl_1.45-1_all.deb ... Unpacking libtext-diff-perl (1.45-1) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../85-libtest-differences-perl_0.67-1_all.deb ... Unpacking libtest-differences-perl (0.67-1) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../86-libtest-exception-perl_0.43-1_all.deb ... Unpacking libtest-exception-perl (0.43-1) ... Selecting previously unselected package libtest-files-perl. Preparing to unpack .../87-libtest-files-perl_0.15-1_all.deb ... Unpacking libtest-files-perl (0.15-1) ... Selecting previously unselected package libtest-warn-perl. 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Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libdata-optlist-perl (0.110-1.1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libmro-compat-perl (0.13-1) ... Setting up libsub-exporter-perl (0.987-1) ... Setting up libeval-closure-perl (0.14-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:armhf (1.11-4) ... Setting up libtest-most-perl (0.37-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up dh-autoreconf (20) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libdist-checkconflicts-perl (0.11-1.1) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.39-1) ... Setting up debhelper (13.3.4) ... Setting up libmodule-runtime-conflicts-perl (0.003-1.1) ... Setting up libclass-load-perl (0.25-1) ... Setting up libpackage-deprecationmanager-perl (0.17-1.1) ... Setting up libdevel-overloadinfo-perl (0.005-1) ... Setting up libclass-load-xs-perl (0.10-1+b5) ... Setting up libmoose-perl (2.2014-2) ... Processing triggers for libc-bin (2.31-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 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 armhf libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 1s (72.3 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 ... 23732 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 ... 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I: Building the package hostname: Name or service not known I: Running cd /build/bio-tradis-1.4.5+dfsg2/ && 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 > ../bio-tradis_1.4.5+dfsg2-1_source.changes dpkg-buildpackage: info: source package bio-tradis dpkg-buildpackage: info: source version 1.4.5+dfsg2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build make: 'build' is up to date. fakeroot debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/bio-tradis-1.4.5+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/build/bio-tradis-1.4.5+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" Checking if your kit is complete... Warning: the following files are missing in your kit: BioTraDISTutorial.pdf Please inform the author. Generating a Unix-style Makefile Writing Makefile for Bio::Tradis Writing MYMETA.yml and MYMETA.json dh_auto_build make -j4 make[1]: ingresso nella directory «/build/bio-tradis-1.4.5+dfsg2» cp lib/Bio/Tradis/AddTagsToSeq.pm blib/lib/Bio/Tradis/AddTagsToSeq.pm cp lib/Bio/Tradis/Samtools.pm blib/lib/Bio/Tradis/Samtools.pm cp lib/Bio/Tradis/CommandLine/TradisAnalysis.pm blib/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm cp lib/Bio/Tradis/TradisPlot.pm blib/lib/Bio/Tradis/TradisPlot.pm cp lib/Bio/Tradis/CommandLine/FilterFastqTags.pm blib/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm cp lib/Bio/Tradis/Parser/Fastq.pm blib/lib/Bio/Tradis/Parser/Fastq.pm cp lib/Bio/Tradis/CommandLine/TradisBam.pm blib/lib/Bio/Tradis/CommandLine/TradisBam.pm cp lib/Bio/Tradis/FilterTags.pm blib/lib/Bio/Tradis/FilterTags.pm cp lib/Bio/Tradis/CommandLine/PlotCombine.pm blib/lib/Bio/Tradis/CommandLine/PlotCombine.pm cp lib/Bio/Tradis/Map.pm blib/lib/Bio/Tradis/Map.pm cp lib/Bio/Tradis/Analysis/InsertSite.pm blib/lib/Bio/Tradis/Analysis/InsertSite.pm cp lib/Bio/Tradis/RunTradis.pm blib/lib/Bio/Tradis/RunTradis.pm cp lib/Bio/Tradis/CommandLine/AddTags.pm blib/lib/Bio/Tradis/CommandLine/AddTags.pm cp lib/Bio/Tradis/CommandLine/PlotTradis.pm blib/lib/Bio/Tradis/CommandLine/PlotTradis.pm cp lib/Bio/Tradis/CommandLine/CheckTags.pm blib/lib/Bio/Tradis/CommandLine/CheckTags.pm cp lib/Bio/Tradis/Parser/Cigar.pm blib/lib/Bio/Tradis/Parser/Cigar.pm cp lib/Bio/Tradis/Parser/Bam.pm blib/lib/Bio/Tradis/Parser/Bam.pm cp lib/Bio/Tradis/CommandLine/RunMapping.pm blib/lib/Bio/Tradis/CommandLine/RunMapping.pm cp lib/Bio/Tradis/CombinePlots.pm blib/lib/Bio/Tradis/CombinePlots.pm cp lib/Bio/Tradis/DetectTags.pm blib/lib/Bio/Tradis/DetectTags.pm cp lib/Bio/Tradis/RemoveTags.pm blib/lib/Bio/Tradis/RemoveTags.pm cp lib/Bio/Tradis.pm blib/lib/Bio/Tradis.pm cp lib/Bio/Tradis/Exception.pm blib/lib/Bio/Tradis/Exception.pm cp lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm blib/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm cp lib/Bio/Tradis/Analysis/Exceptions.pm blib/lib/Bio/Tradis/Analysis/Exceptions.pm cp bin/add_tradis_tags blib/script/add_tradis_tags cp bin/bacteria_tradis blib/script/bacteria_tradis cp bin/check_tradis_tags blib/script/check_tradis_tags cp bin/combine_tradis_plots blib/script/combine_tradis_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/add_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bacteria_tradis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/check_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/combine_tradis_plots cp bin/filter_tradis_tags blib/script/filter_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/filter_tradis_tags cp bin/remove_tradis_tags blib/script/remove_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/remove_tradis_tags cp bin/tradis_comparison.R blib/script/tradis_comparison.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_comparison.R cp bin/tradis_essentiality.R blib/script/tradis_essentiality.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_essentiality.R cp bin/tradis_gene_insert_sites blib/script/tradis_gene_insert_sites "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_gene_insert_sites cp bin/tradis_merge_plots blib/script/tradis_merge_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_merge_plots cp bin/tradis_plot blib/script/tradis_plot "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_plot Manifying 9 pod documents Manifying 25 pod documents make[1]: uscita dalla directory «/build/bio-tradis-1.4.5+dfsg2» debian/rules override_dh_auto_test make[1]: ingresso nella directory «/build/bio-tradis-1.4.5+dfsg2» dh_auto_test || true make -j4 test TEST_VERBOSE=1 make[2]: ingresso nella directory «/build/bio-tradis-1.4.5+dfsg2» PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/Bio/Tradis/*.t t/Bio/Tradis/Analysis/*.t t/Bio/Tradis/CommandLine/*.t t/Bio/Tradis/Parser/*.t # # Versions for all modules listed in MYMETA.json (including optional ones): # # === Configure Requires === # # Module Want Have # ------------------- ---- ---- # ExtUtils::MakeMaker any 7.44 # # === Build Requires === # # Module Want Have # ------------------- ---- ---- # ExtUtils::MakeMaker any 7.44 # # === Test Requires === # # Module Want Have # ------------------- ---- -------- # Env::Path 0.18 0.19 # ExtUtils::MakeMaker any 7.44 # File::Spec any 3.78 # Test::Exception any 0.43 # Test::Files any 0.15 # Test::More any 1.302175 # Test::Most any 0.37 # # === Test Recommends === # # Module Want Have # ---------- -------- -------- # CPAN::Meta 2.120900 2.150010 # # === Runtime Requires === # # Module Want Have # ---------------- ---- -------- # Bio::Seq any 1.7.7 # Bio::SeqIO any 1.7.7 # Cwd any 3.78 # Data::Dumper any 2.174_01 # Exception::Class any 1.44 # File::Basename any 2.85 # File::Path any 2.16 # File::Spec any 3.78 # File::Temp any 0.2309 # FindBin any 1.51 # Getopt::Long any 2.51 # Moose any 2.2014 # Text::CSV any 2.00 # Try::Tiny any 0.30 # strict any 1.11 # warnings any 1.47 # t/00-report-prereqs.t ...................... 1..1 ok 1 ok # Failed test 'checking file contents' # at t/Bio/Tradis/AddTagsToSeq.t line 37. # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # | |Got | |Expected | # | Ln| | Ln| | # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # | 15|@PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' | 15|@PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' | # | 16|@PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | 16|@PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | # | 17|@PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 | 17|@PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 | # * 18|@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.11 CL:samtools view -H t/data/AddTags/sample_sm_tr.bam * 18|@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.11 CL:samtools view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.bam * # * 19|@PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools view -h -S -b -o t/data/output.bam tmp.20210712193322.sam * | | # * 20|@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.11 CL:samtools view -h -o t/data/output.sam t/data/output.bam * | | # | 21|MS5_9521:1:1101:10072:14269#14 16 ENA|AE004091|AE004091.2 5 37 60M * 0 0 AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACCCTGACTCTTA HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABAFFFFFBBCCC X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:BBCDECBC XT:A:U tq:Z:CCCBBFFFFF tr:Z:TAAGAGTCAG | 19|MS5_9521:1:1101:10072:14269#14 16 ENA|AE004091|AE004091.2 5 37 60M * 0 0 AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACCCTGACTCTTA HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABAFFFFFBBCCC X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:BBCDECBC XT:A:U tq:Z:CCCBBFFFFF tr:Z:TAAGAGTCAG | # | 22|MS5_9521:1:1103:26809:18585#14 1040 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA 5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3FFFFFCCCCB X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:CCCCCCCC XT:A:U tq:Z:BCCCCFFFFF tr:Z:TAAGAGTCAG | 20|MS5_9521:1:1103:26809:18585#14 1040 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA 5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3FFFFFCCCCB X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:CCCCCCCC XT:A:U tq:Z:BCCCCFFFFF tr:Z:TAAGAGTCAG | # | 23|MS5_9521:1:2101:3627:15042#14 16 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA HHHGHHHGHHGGHHHHHHHHHHHHHHGGGGGGGGGGGGFFCFFFFBBBAAFFFFFCBAAA X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:AAA>AAAA XT:A:U tq:Z:AAABCFFFFF tr:Z:TAAGAGTCAG | 21|MS5_9521:1:2101:3627:15042#14 16 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA HHHGHHHGHHGGHHHHHHHHHHHHHHGGGGGGGGGGGGFFCFFFFBBBAAFFFFFCBAAA X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:AAA>AAAA XT:A:U tq:Z:AAABCFFFFF tr:Z:TAAGAGTCAG | # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # Failed test 'checking file contents' # at t/Bio/Tradis/AddTagsToSeq.t line 57. # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # | |Got | |Expected | # | Ln| | Ln| | # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # | 15|@PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' | 15|@PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' | # | 16|@PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | 16|@PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | # | 17|@PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 | 17|@PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 | # * 18|@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.11 CL:samtools view -h -o t/data/AddTags/sample_sm_no_tr.sam t/data/AddTags/sample_sm_no_tr.bam * 18|@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.11 CL:samtools view -H t/data/AddTags/sample_sm_tr.bam * # | | * 19|@PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools view -h -S -b -o t/data/output.bam tmp.20210712193322.sam * # | | * 20|@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.11 CL:samtools view -h -o t/data/output.sam t/data/output.bam * # | 19|MS5_9521:1:1101:10072:14269#14 16 ENA|AE004091|AE004091.2 5 37 60M * 0 0 AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACCCTGACTCTTA HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABAFFFFFBBCCC X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:BBCDECBC XT:A:U tq:Z:CCCBBFFFFF tr:Z:TAAGAGTCAG | 21|MS5_9521:1:1101:10072:14269#14 16 ENA|AE004091|AE004091.2 5 37 60M * 0 0 AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACCCTGACTCTTA HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABAFFFFFBBCCC X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:BBCDECBC XT:A:U tq:Z:CCCBBFFFFF tr:Z:TAAGAGTCAG | # | 20|MS5_9521:1:1103:26809:18585#14 1040 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA 5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3FFFFFCCCCB X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:CCCCCCCC XT:A:U tq:Z:BCCCCFFFFF tr:Z:TAAGAGTCAG | 22|MS5_9521:1:1103:26809:18585#14 1040 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA 5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3FFFFFCCCCB X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:CCCCCCCC XT:A:U tq:Z:BCCCCFFFFF tr:Z:TAAGAGTCAG | # | 21|MS5_9521:1:2101:3627:15042#14 16 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA HHHGHHHGHHGGHHHHHHHHHHHHHHGGGGGGGGGGGGFFCFFFFBBBAAFFFFFCBAAA X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:AAA>AAAA XT:A:U tq:Z:AAABCFFFFF tr:Z:TAAGAGTCAG | 23|MS5_9521:1:2101:3627:15042#14 16 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA HHHGHHHGHHGGHHHHHHHHHHHHHHGGGGGGGGGGGGFFCFFFFBBBAAFFFFFCBAAA X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:AAA>AAAA XT:A:U tq:Z:AAABCFFFFF tr:Z:TAAGAGTCAG | # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Protocol not supported [E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta [E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta' [E::cram_get_ref] Failed to populate reference for id 0 [E::cram_decode_slice] Unable to fetch reference #0:5-193 [E::cram_next_slice] Failure to decode slice samtools view: error reading file "t/data/AddTags/sample_sm_tr.cram": No such file or directory [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Protocol not supported [E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta [E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta' [E::cram_get_ref] Failed to populate reference for id 0 [E::cram_decode_slice] Unable to fetch reference #0:5-193 [E::cram_next_slice] Failure to decode slice samtools view: error reading file "t/data/AddTags/sample_sm_tr.cram": No such file or directory [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Protocol not supported [E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta [E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta' [E::cram_get_ref] Failed to populate reference for id 0 [E::cram_decode_slice] Unable to fetch reference #0:5-203 [E::cram_next_slice] Failure to decode slice samtools view: error reading file "t/data/AddTags/expected_tradis.cram": No such file or directory # Failed test 'checking file contents' # at t/Bio/Tradis/AddTagsToSeq.t line 86. # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # | |Got | |Expected | # | Ln| | Ln| | # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # | 1|@HD VN:1.4 SO:coordinate | 1|@HD VN:1.4 SO:coordinate | # | | * 2|@RG ID:1#14 PL:ILLUMINA PU:130320_MS5_9521_A_MS0205701-050V2_1#14 LB:6982965 DS:ERP002335: http://www.sanger.ac.uk/resources/downloads/bacteria/citrobacter-rodentium.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2013-03-20T00:00:00+0000 SM:ERS222909 CN:SC * # | | * 3|@SQ SN:ENA|AE004091|AE004091.2 LN:6264404 UR:file:/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta AS:PAO1 M5:7f8b730b8a08ebf1eeb7f0de561f0a91 SP:Pseudomonas aeruginosa * # | 2|@PG ID:SCS PN:MiSeq Control Software DS:Controlling software on instrument VN:2.2.0 | 4|@PG ID:SCS PN:MiSeq Control Software DS:Controlling software on instrument VN:2.2.0 | # | 3|@PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.28.0 | 5|@PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.28.0 | # | 4|@PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.10 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=ERS222824,ERS222825,ERS222825,ERS222824,ERS222909,ERS222910 LIBRARY_NAME=6983166 STUDY_NAME=ERP002335: http://www.sanger.ac.uk/resources/downloads/bacteria/citrobacter-rodentium.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ BARCODE_SEQUENCE_TAG_NAME=tr BARCODE_QUALITY_TAG_NAME=tq SECOND_BARCODE_SEQUENCE_TAG_NAME=BC SECOND_BARCODE_QUALITY_TAG_NAME=QT COMPRESSION_LEVEL=0 CREATE_MD5_FILE=true GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 SEQUENCING_CENTER=SC PLATFORM=ILLUMINA VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | 6|@PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.10 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=ERS222824,ERS222825,ERS222825,ERS222824,ERS222909,ERS222910 LIBRARY_NAME=6983166 STUDY_NAME=ERP002335: http://www.sanger.ac.uk/resources/downloads/bacteria/citrobacter-rodentium.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ BARCODE_SEQUENCE_TAG_NAME=tr BARCODE_QUALITY_TAG_NAME=tq SECOND_BARCODE_SEQUENCE_TAG_NAME=BC SECOND_BARCODE_QUALITY_TAG_NAME=QT COMPRESSION_LEVEL=0 CREATE_MD5_FILE=true GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 SEQUENCING_CENTER=SC PLATFORM=ILLUMINA VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false | # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # | 13|@PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' | 15|@PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' | # | 14|@PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | 16|@PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | # | 15|@PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 | 17|@PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 | # * 16|@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.11 CL:samtools view -H t/data/AddTags/sample_sm_tr.cram * 18|@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.11 CL:samtools view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.cram * # * 17|@PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools view -h -S -C -o t/data/output.cram tmp.20210712193322.sam * | | # * 18|@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.11 CL:samtools view -h -o t/data/output.sam t/data/output.cram * | | # * 19|@SQ SN:ENA|AE004091|AE004091.2 LN:6264404 UR:file:/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta AS:PAO1 M5:7f8b730b8a08ebf1eeb7f0de561f0a91 SP:Pseudomonas aeruginosa * | | # * 20|@RG ID:1#14 PL:ILLUMINA PU:130320_MS5_9521_A_MS0205701-050V2_1#14 LB:6982965 DS:ERP002335: http://www.sanger.ac.uk/resources/downloads/bacteria/citrobacter-rodentium.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2013-03-20T00:00:00+0000 SM:ERS222909 CN:SC * | | # +---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ # Looks like you failed 3 tests of 15. t/Bio/Tradis/AddTagsToSeq.t ................ ok 1 - use Bio::Tradis::AddTagsToSeq; ok 2 - creating object ok 3 - correctly select the bam output switch ok 4 - testing output ok 5 - checking file existence not ok 6 - checking file contents ok 7 - creating object ok 8 - checking file existence not ok 9 - checking file contents ok 10 - number of reads as expected ok 11 - creating object with cram file ok 12 - correctly select the cram output switch ok 13 - testing output ok 14 - checking file existence not ok 15 - checking file contents 1..15 Dubious, test returned 3 (wstat 768, 0x300) Failed 3/15 subtests t/Bio/Tradis/Analysis/InsertSite.t ......... ok 1 - use Bio::Tradis::Analysis::InsertSite; ok 2 ok 3 ok 4 - check main sequence insert_site values first value ok 5 - check main sequence insert_site value before site ok 6 - check main sequence insert_site values for reverse reads only ok 7 - various values ok 8 - various values ok 9 - various values ok 10 - various values ok 11 - various values ok 12 - check empty plasmid insert_site values first value ok 13 - check empty plasmid insert_site values last value ok 14 - check plasmid with 1 read insert_site values first value ok 15 - check plasmid with 1 read insert_site values first base of read ok 16 - check plasmid with 1 read insert_site values after last base of read ok 17 - check plasmid with 1 read insert_site values last value ok 18 - check another empty plasmid insert_site values first value ok 19 - check another empty plasmid insert_site values last value ok 20 ok 21 ok 22 - check forward read ok 23 - check reverse read 1..23 ok [tabix] the index file exists. Please use '-f' to overwrite. t/Bio/Tradis/CombinePlots.t ................ ok 1 - use Bio::Tradis::CombinePlots; ok 2 - creating object ok 3 - combining plots ok 4 - checking first combined plot file exists ok 5 - checking second combined plot file exists ok 6 - checking stats file exists ok 7 - checking first file contents ok 8 - checking second file contents ok 9 - checking stats file contents ok 10 - creating object ok 11 - combining plots ok 12 - checking first combined plot file exists ok 13 - checking tabix sorted combined plot file exists ok 14 - checking tabix index file exists ok 15 - checking zipped file contents ok 16 - checking stats file contents ok 17 - creating object ok 18 - combining plots ok 19 - checking directory exists ok 20 - checking first combined plot file exists ok 21 - checking second combined plot file exists 1..21 ok Attribute (_stats_handle) does not pass the type constraint because: Validation failed for 'FileHandle' with value GLOB(0x35af248) at reader Bio::Tradis::CommandLine::TradisAnalysis::_stats_handle (defined at lib/Bio/Tradis/CommandLine/TradisAnalysis.pm line 43) line 15 Bio::Tradis::CommandLine::TradisAnalysis::_stats_handle('Bio::Tradis::CommandLine::TradisAnalysis=HASH(0x3485720)') called at lib/Bio/Tradis/CommandLine/TradisAnalysis.pm line 146 Bio::Tradis::CommandLine::TradisAnalysis::run('Bio::Tradis::CommandLine::TradisAnalysis=HASH(0x3485720)') called at t/Bio/Tradis/CommandLine/TradisAnalysis.t line 33 # Tests were run but no plan was declared and done_testing() was not seen. # Looks like your test exited with 255 just after 2. t/Bio/Tradis/CommandLine/TradisAnalysis.t .. ok 1 - use Bio::Tradis::CommandLine::TradisAnalysis; ok 2 - creating object Dubious, test returned 255 (wstat 65280, 0xff00) All 2 subtests passed [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Protocol not supported t/Bio/Tradis/DetectTags.t .................. ok 1 - use Bio::Tradis::DetectTags; ok 2 - testing tag checker - tradis ok 3 - testing output ok 4 - testing tag checker for cram- tradis ok 5 - testing output cram ok 6 - testing tag checker - no tradis ok 7 - testing output 1..7 ok t/Bio/Tradis/FilterTags.t .................. ok 1 - use Bio::Tradis::FilterTags; ok 2 - creating object ok 3 - testing output ok 4 - checking file existence ok 5 - checking file contents ok 6 - creating object ok 7 - testing output ok 8 - checking file existence ok 9 - checking file contents ok 10 - creating object ok 11 - testing output ok 12 - checking file existence ok 13 - checking file contents ok 14 - creating object ok 15 - testing output ok 16 - checking file existence ok 17 - checking file contents 1..17 ok t/Bio/Tradis/Map.t ......................... ok 1 - use Bio::Tradis::Map; ok 2 - creating object ok 3 - testing reference indexing ok 4 - checking index file existence ok 5 - checking index file existence ok 6 - testing smalt mapping ok 7 - checking index file existence ok 8 - checking file contents ok 9 - creating object ok 10 - testing reference indexing ok 11 - checking index file existence ok 12 - checking index file existence ok 13 - checking index file existence ok 14 - checking index file existence ok 15 - checking index file existence ok 16 - testing bwa mapping ok 17 - checking index file existence ok 18 - checking file contents ok 19 - creating object ok 20 - indexing args correct ok 21 - mapping args correct 1..21 ok t/Bio/Tradis/Parser/Bam.t .................. ok 1 - use Bio::Tradis::Parser::Bam; ok 2 - creating object ok 3 - An object of class 'Bio::Tradis::Parser::Bam' isa 'Bio::Tradis::Parser::Bam' ok 4 - seq_info returns a hash ok 5 - first result detected ok 6 - read_info contains correct info for first line ok 7 - testing flag parsing - mapped ok 8 - testing flag parsing - reverse complement ok 9 - last result detected ok 10 - read_info contains correct info for last line ok 11 - EOF detected 1..11 ok t/Bio/Tradis/Parser/Cigar.t ................ ok 1 - use Bio::Tradis::Parser::Cigar; ok 2 - initialise obj -all matching ok 3 - read start -all matching ok 4 - read end -all matching ok 5 - initialise obj -nothing matching ok 6 - read start -nothing matching ok 7 - read end -nothing matching ok 8 - initialise obj -soft clipping at start ok 9 - read start -soft clipping at start ok 10 - read end -soft clipping at start ok 11 - initialise obj -soft clipping at end ok 12 - read start -soft clipping at end ok 13 - read end -soft clipping at end ok 14 - initialise obj -soft clipping at both ends ok 15 - read start -soft clipping at both ends ok 16 - read end -soft clipping at both ends ok 17 - initialise obj -deletion in middle ok 18 - read start -deletion in middle ok 19 - read end -deletion in middle ok 20 - initialise obj -insertions and deletions ok 21 - read start -insertions and deletions ok 22 - read end -insertions and deletions ok 23 - initialise obj -insertions in the middle ok 24 - read start -insertions in the middle ok 25 - read end -insertions in the middle 1..25 ok t/Bio/Tradis/Parser/Fastq.t ................ ok 1 - use Bio::Tradis::Parser::Fastq; ok 2 - creating object ok 3 - An object of class 'Bio::Tradis::Parser::Fastq' isa 'Bio::Tradis::Parser::Fastq' ok 4 - first result detected ok 5 - read_info contains correct info for first line ok 6 - last result detected ok 7 - read_info contains correct info for last line ok 8 - EOF detected 1..8 ok t/Bio/Tradis/RemoveTags.t .................. ok 1 - use Bio::Tradis::RemoveTags; ok 2 - creating object ok 3 - testing output ok 4 - checking file existence ok 5 - checking file contents ok 6 - creating object ok 7 - testing output ok 8 - checking file existence ok 9 - checking file contents ok 10 - creating object ok 11 - testing output ok 12 - checking file existence ok 13 - checking file contents 1..13 ok t/Bio/Tradis/RunTradisBWA.t ................ ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing filtering step ok 4 - checking filtered file existence - Normal files, no mismatch ok 5 - checking filtered file contents - Normal files, no mismatch ok 6 - testing check filtering step ok 7 - complain if no filtered reads ok 8 - complain if filtered reads are empty ok 9 - complain if filtered reads has less than 4 lines ok 10 - complain if filtered reads do not look like a fastq ok 11 - complain if filtered reads are too short ok 12 - check very basic filtered reads validation ok 13 - testing tag removal ok 14 - checking de-tagged file existence - Normal files, no mismatch ok 15 - checking de-tagged file contents - Normal files, no mismatch ok 16 - testing mapping ok 17 - checking SAM existence ok 18 - checking mapped file contents ok 19 - testing SAM/BAM conversion ok 20 - checking BAM existence ok 21 - testing BAM sorting ok 22 - checking sorted BAM existence - Normal files, no mismatch ok 23 - checking indexed BAM existence - Normal files, no mismatch ok 24 - testing bamcheck ok 25 - checking bamcheck file existence - Normal files, no mismatch ok 26 - testing plotting ok 27 - checking plot file existence - Normal files, no mismatch ok 28 - checking plot file contents - Normal files, no mismatch ok 29 - testing complete analysis - Normal files, no mismatch ok 30 - checking plot file existence - Normal files, no mismatch ok 31 - checking completed pipeline file contents - Normal files, no mismatch ok 32 - creating object - Normal files one mismatch ok 33 - testing complete analysis with mismatch ok 34 - checking plot file existence - Normal files one mismatch ok 35 - checking completed pipeline with mismatch file contents - Normal files one mismatch ok 36 - creating object with gzipped data - Normal files one mismatch ok 37 - testing complete analysis with gzipped data ok 38 - checking plot file existence (gzipped data) - Normal files one mismatch ok 39 - checking mapped bam existence - Normal files one mismatch ok 40 - checking indexed bam file - Normal files one mismatch ok 41 - checking completed pipeline with gzipped data file contents - Normal files one mismatch ok 42 - creating object with custom smalt parameters ok 43 - mapping with custom parameters fine ok 44 - creating object ok 45 - correct error thrown 1..45 ok t/Bio/Tradis/RunTradisSmalt.t .............. ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing filtering step ok 4 - checking filtered file existence - Normal files, no mismatch ok 5 - checking filtered file contents - Normal files, no mismatch ok 6 - testing check filtering step ok 7 - complain if no filtered reads ok 8 - complain if filtered reads are empty ok 9 - complain if filtered reads has less than 4 lines ok 10 - complain if filtered reads do not look like a fastq ok 11 - complain if filtered reads are too short ok 12 - check very basic filtered reads validation ok 13 - testing tag removal ok 14 - checking de-tagged file existence - Normal files, no mismatch ok 15 - checking de-tagged file contents - Normal files, no mismatch ok 16 - testing mapping ok 17 - checking SAM existence ok 18 - checking mapped file contents ok 19 - testing SAM/BAM conversion ok 20 - checking BAM existence ok 21 - testing BAM sorting ok 22 - checking sorted BAM existence - Normal files, no mismatch ok 23 - checking indexed BAM existence - Normal files, no mismatch ok 24 - testing bamcheck ok 25 - checking bamcheck file existence - Normal files, no mismatch ok 26 - testing plotting ok 27 - checking plot file existence - Normal files, no mismatch ok 28 - checking plot file contents - Normal files, no mismatch ok 29 - testing complete analysis - Normal files, no mismatch ok 30 - checking plot file existence - Normal files, no mismatch ok 31 - checking completed pipeline file contents - Normal files, no mismatch ok 32 - creating object - Normal files one mismatch ok 33 - testing complete analysis with mismatch ok 34 - checking plot file existence - Normal files one mismatch ok 35 - checking completed pipeline with mismatch file contents - Normal files one mismatch ok 36 - creating object with gzipped data - Normal files one mismatch ok 37 - testing complete analysis with gzipped data ok 38 - checking plot file existence (gzipped data) - Normal files one mismatch ok 39 - checking mapped bam existence - Normal files one mismatch ok 40 - checking indexed bam file - Normal files one mismatch ok 41 - checking completed pipeline with gzipped data file contents - Normal files one mismatch ok 42 - creating object with custom smalt parameters ok 43 - mapping with custom parameters fine ok 44 - creating object with custom smalt parameters ok 45 - correct error thrown 1..45 ok t/Bio/Tradis/RunTradisTaglessBwa.t ......... ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing mapping ok 4 - checking SAM existence ok 5 - checking mapped file contents ok 6 - testing SAM/BAM conversion ok 7 - checking BAM existence ok 8 - testing BAM sorting ok 9 - checking sorted BAM existence - Normal files, no mismatch ok 10 - checking indexed BAM existence - Normal files, no mismatch ok 11 - testing bamcheck ok 12 - checking bamcheck file existence - Normal files, no mismatch ok 13 - testing plotting ok 14 - checking plot file existence - Normal files, no mismatch ok 15 - checking plot file contents - Normal files, no mismatch ok 16 - testing complete analysis - Normal files, no mismatch ok 17 - checking plot file existence - Normal files, no mismatch ok 18 - checking completed pipeline file contents - Normal files, no mismatch ok 19 - creating object with custom smalt parameters ok 20 - mapping with custom parameters fine ok 21 - creating object ok 22 - correct error thrown 1..22 ok t/Bio/Tradis/RunTradisTaglessSmalt.t ....... ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing mapping ok 4 - checking SAM existence ok 5 - checking mapped file contents ok 6 - testing SAM/BAM conversion ok 7 - checking BAM existence ok 8 - testing BAM sorting ok 9 - checking sorted BAM existence - Normal files, no mismatch ok 10 - checking indexed BAM existence - Normal files, no mismatch ok 11 - testing bamcheck ok 12 - checking bamcheck file existence - Normal files, no mismatch ok 13 - testing plotting ok 14 - checking plot file existence - Normal files, no mismatch ok 15 - checking plot file contents - Normal files, no mismatch ok 16 - testing complete analysis - Normal files, no mismatch ok 17 - checking plot file existence - Normal files, no mismatch ok 18 - checking completed pipeline file contents - Normal files, no mismatch ok 19 - creating object with custom smalt parameters ok 20 - mapping with custom parameters fine ok 21 - creating object with custom smalt parameters ok 22 - correct error thrown 1..22 ok t/Bio/Tradis/TradisPlot.t .................. ok 1 - use Bio::Tradis::TradisPlot; ok 2 - creating object ok 3 - testing plotting ok 4 - checking plot file existence ok 5 - checking file contents 1..5 ok t/requires_external.t ...................... 1..6 ok 1 - awk in PATH ok 2 - samtools in PATH ok 3 - gunzip in PATH ok 4 - gzip in PATH ok 5 - smalt in PATH ok 6 - tabix in PATH ok Test Summary Report ------------------- t/Bio/Tradis/AddTagsToSeq.t (Wstat: 768 Tests: 15 Failed: 3) Failed tests: 6, 9, 15 Non-zero exit status: 3 t/Bio/Tradis/CommandLine/TradisAnalysis.t (Wstat: 65280 Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: No plan found in TAP output Files=18, Tests=309, 24 wallclock secs ( 0.19 usr 0.08 sys + 17.43 cusr 5.76 csys = 23.46 CPU) Result: FAIL Failed 2/18 test programs. 3/309 subtests failed. make[2]: *** [Makefile:1078: test_dynamic] Errore 255 make[2]: uscita dalla directory «/build/bio-tradis-1.4.5+dfsg2» dh_auto_test: error: make -j4 test TEST_VERBOSE=1 returned exit code 2 make[1]: uscita dalla directory «/build/bio-tradis-1.4.5+dfsg2» create-stamp debian/debhelper-build-stamp dh_testroot dh_prep dh_auto_install make -j4 install DESTDIR=/build/bio-tradis-1.4.5\+dfsg2/debian/bio-tradis AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: ingresso nella directory «/build/bio-tradis-1.4.5+dfsg2» Manifying 9 pod documents Manifying 25 pod documents Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/FilterTags.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/DetectTags.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CombinePlots.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/AddTagsToSeq.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/RemoveTags.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/TradisPlot.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Exception.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Samtools.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Map.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/RunTradis.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Fastq.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Bam.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Cigar.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/AddTags.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RemoveFastqTags.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisAnalysis.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotTradis.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/FilterFastqTags.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotCombine.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RunMapping.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisBam.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/CheckTags.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/InsertSite.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/Exceptions.pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/tradis_gene_insert_sites.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/combine_tradis_plots.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/filter_tradis_tags.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/check_tradis_tags.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/tradis_plot.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/add_tradis_tags.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/remove_tradis_tags.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/bacteria_tradis.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::Exceptions.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotCombine.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::AddTags.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotTradis.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisBam.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Samtools.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Bam.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::TradisPlot.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::InsertSite.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Map.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RemoveFastqTags.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::FilterTags.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RunTradis.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisAnalysis.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::AddTagsToSeq.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CombinePlots.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::DetectTags.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::CheckTags.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Cigar.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::FilterFastqTags.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Exception.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Fastq.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RemoveTags.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RunMapping.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis.3pm Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/filter_tradis_tags Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/bacteria_tradis Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_gene_insert_sites Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/combine_tradis_plots Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_comparison.R Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_essentiality.R Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/remove_tradis_tags Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/check_tradis_tags Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_plot Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/add_tradis_tags Installing /build/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_merge_plots make[1]: uscita dalla directory «/build/bio-tradis-1.4.5+dfsg2» debian/rules override_dh_install make[1]: ingresso nella directory «/build/bio-tradis-1.4.5+dfsg2» dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done mv debian/bio-tradis/usr/bin/tradis_comparison.R debian/bio-tradis/usr/bin/tradis_comparison mv debian/bio-tradis/usr/bin/tradis_essentiality.R debian/bio-tradis/usr/bin/tradis_essentiality make[1]: uscita dalla directory «/build/bio-tradis-1.4.5+dfsg2» dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: ingresso nella directory «/build/bio-tradis-1.4.5+dfsg2» dh_installman rm debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p* make[1]: uscita dalla directory «/build/bio-tradis-1.4.5+dfsg2» dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: generazione del pacchetto "bio-tradis" in "../bio-tradis_1.4.5+dfsg2-1_all.deb". dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bio-tradis_1.4.5+dfsg2-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/822/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/822/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/822 and its subdirectories I: Current time: Mon Jul 12 19:33:53 +14 2021 I: pbuilder-time-stamp: 1626068033