I: pbuilder: network access will be disabled during build
I: Current time: Tue Dec 17 15:52:42 -12 2024
I: pbuilder-time-stamp: 1734493962
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
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: using eatmydata during job
I: Copying source file
I: copying [bio-tradis_1.4.5+dfsg2-2.dsc]
I: copying [./bio-tradis_1.4.5+dfsg2.orig.tar.xz]
I: copying [./bio-tradis_1.4.5+dfsg2-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Jan 25 14:37:55 2024
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./bio-tradis_1.4.5+dfsg2-2.dsc: no acceptable signature found
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+dfsg2-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying samtools1.10
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/27270/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='958af384e84247bd9f68d86844abeb57'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='27270'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Zeli6c3x/pbuilderrc_jbqr --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Zeli6c3x/b1 --logfile b1/build.log bio-tradis_1.4.5+dfsg2-2.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos2-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/27270/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), 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 ... 19952 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on 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} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconst-fast-perl{a} libcurl3t64-gnutls{a} libdata-compare-perl{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} libelf1t64{a} libenv-path-perl{a} libeval-closure-perl{a} libexception-class-perl{a} libfile-chdir-perl{a} libfile-find-rule-perl{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libio-string-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{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} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnumber-compare-perl{a} libpackage-deprecationmanager-perl{a} libpackage-stash-perl{a} libpackage-stash-xs-perl{a} libpadwalker-perl{a} libparams-classify-perl{a} libparams-util-perl{a} libpath-tiny-perl{a} libpipeline1{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-install-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} libtest2-suite-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtext-glob-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 krb5-locales 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 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 libmodule-pluggable-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 libunicode-utf8-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, 111 newly installed, 0 to remove and 0 not upgraded.
Need to get 30.1 MB of archives. After unpacking 106 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-3 [201 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-3 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 bwa i386 0.7.18-1 [237 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.21 [88.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 23 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-3 [1631 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.21 [919 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 libalgorithm-c3-perl all 0.11-2 [10.8 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libb-hooks-op-check-perl i386 0.22-3+b2 [10.7 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 libbambamc0 i386 0.0.50-6+b2 [43.7 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 libio-string-perl all 1.08-4 [12.1 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libdata-stag-perl all 0.14-3 [448 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 libclass-c3-perl all 0.35-2 [21.0 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 libclass-data-inheritable-perl all 0.10-1 [8632 B]
Get: 42 http://deb.debian.org/debian unstable/main i386 libparams-util-perl i386 1.102-3+b1 [24.7 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 libsub-install-perl all 0.929-1 [10.5 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 libdevel-callchecker-perl i386 0.009-1+b1 [16.2 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 libparams-classify-perl i386 0.015-2+b4 [23.1 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 libclass-load-perl all 0.25-2 [15.3 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 libclass-load-xs-perl i386 0.10-2+b4 [14.3 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 libclass-xsaccessor-perl i386 1.19-4+b4 [37.5 kB]
Get: 55 http://deb.debian.org/debian unstable/main i386 libclone-perl i386 0.47-1+b1 [14.0 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get: 59 http://deb.debian.org/debian unstable/main i386 libconst-fast-perl all 0.014-2 [8792 B]
Get: 60 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB]
Get: 61 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB]
Get: 62 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 63 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB]
Get: 64 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB]
Get: 66 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB]
Get: 67 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 69 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 70 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.1-1 [404 kB]
Get: 76 http://deb.debian.org/debian unstable/main i386 libnumber-compare-perl all 0.03-3 [6332 B]
Get: 77 http://deb.debian.org/debian unstable/main i386 libtext-glob-perl all 0.11-3 [7676 B]
Get: 78 http://deb.debian.org/debian unstable/main i386 libfile-find-rule-perl all 0.34-3 [26.6 kB]
Get: 79 http://deb.debian.org/debian unstable/main i386 libdata-compare-perl all 1.29-1 [19.6 kB]
Get: 80 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB]
Get: 81 http://deb.debian.org/debian unstable/main i386 libdevel-globaldestruction-perl all 0.14-4 [7144 B]
Get: 82 http://deb.debian.org/debian unstable/main i386 libmro-compat-perl all 0.15-2 [11.8 kB]
Get: 83 http://deb.debian.org/debian unstable/main i386 libdevel-overloadinfo-perl all 0.007-1 [7896 B]
Get: 84 http://deb.debian.org/debian unstable/main i386 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get: 85 http://deb.debian.org/debian unstable/main i386 libdist-checkconflicts-perl all 0.11-2 [10.5 kB]
Get: 86 http://deb.debian.org/debian unstable/main i386 libenv-path-perl all 0.19-4 [19.1 kB]
Get: 87 http://deb.debian.org/debian unstable/main i386 libeval-closure-perl all 0.14-3 [11.2 kB]
Get: 88 http://deb.debian.org/debian unstable/main i386 libexception-class-perl all 1.45-1 [34.6 kB]
Get: 89 http://deb.debian.org/debian unstable/main i386 libfile-chdir-perl all 0.1008-1.2 [11.9 kB]
Get: 90 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB]
Get: 91 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.20+ds-2 [500 kB]
Get: 92 http://deb.debian.org/debian unstable/main i386 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B]
Get: 93 http://deb.debian.org/debian unstable/main i386 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB]
Get: 94 http://deb.debian.org/debian unstable/main i386 libpackage-stash-xs-perl i386 0.30-1+b4 [21.2 kB]
Get: 95 http://deb.debian.org/debian unstable/main i386 libmoose-perl i386 2.2207-1+b2 [767 kB]
Get: 96 http://deb.debian.org/debian unstable/main i386 libncurses6 i386 6.5-2+b1 [112 kB]
Get: 97 http://deb.debian.org/debian unstable/main i386 libpadwalker-perl i386 2.5-1+b6 [19.1 kB]
Get: 98 http://deb.debian.org/debian unstable/main i386 libpath-tiny-perl all 0.146-1 [56.2 kB]
Get: 99 http://deb.debian.org/debian unstable/main i386 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get: 100 http://deb.debian.org/debian unstable/main i386 libtest-deep-perl all 1.204-1 [52.9 kB]
Get: 101 http://deb.debian.org/debian unstable/main i386 libtext-diff-perl all 1.45-2 [27.2 kB]
Get: 102 http://deb.debian.org/debian unstable/main i386 libtest-differences-perl all 0.71-1 [17.9 kB]
Get: 103 http://deb.debian.org/debian unstable/main i386 libtest-exception-perl all 0.43-3 [16.9 kB]
Get: 104 http://deb.debian.org/debian unstable/main i386 libtest2-suite-perl all 0.000163-1 [383 kB]
Get: 105 http://deb.debian.org/debian unstable/main i386 libtest-files-perl all 0.26-1 [21.6 kB]
Get: 106 http://deb.debian.org/debian unstable/main i386 libtest-warn-perl all 0.37-2 [14.5 kB]
Get: 107 http://deb.debian.org/debian unstable/main i386 libtest-most-perl all 0.38-1 [25.1 kB]
Get: 108 http://deb.debian.org/debian unstable/main i386 libtext-csv-perl all 2.04-1 [112 kB]
Get: 109 http://deb.debian.org/debian unstable/main i386 samtools i386 1.20-3 [688 kB]
Get: 110 http://deb.debian.org/debian unstable/main i386 smalt i386 0.7.6-13 [127 kB]
Get: 111 http://deb.debian.org/debian unstable/main i386 tabix i386 1.20+ds-2 [536 kB]
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/bio-tradis-1.4.5+dfsg2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bio-tradis_1.4.5+dfsg2-2_source.changes
dpkg-buildpackage: info: source package bio-tradis
dpkg-buildpackage: info: source version 1.4.5+dfsg2-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bio-tradis-1.4.5+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 -j11
make[1]: Entering directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
cp lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm blib/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm
cp lib/Bio/Tradis/CommandLine/PlotCombine.pm blib/lib/Bio/Tradis/CommandLine/PlotCombine.pm
cp lib/Bio/Tradis/Analysis/InsertSite.pm blib/lib/Bio/Tradis/Analysis/InsertSite.pm
cp lib/Bio/Tradis/Analysis/Exceptions.pm blib/lib/Bio/Tradis/Analysis/Exceptions.pm
cp lib/Bio/Tradis/Parser/Bam.pm blib/lib/Bio/Tradis/Parser/Bam.pm
cp lib/Bio/Tradis.pm blib/lib/Bio/Tradis.pm
cp lib/Bio/Tradis/CommandLine/PlotTradis.pm blib/lib/Bio/Tradis/CommandLine/PlotTradis.pm
cp lib/Bio/Tradis/CommandLine/TradisBam.pm blib/lib/Bio/Tradis/CommandLine/TradisBam.pm
cp lib/Bio/Tradis/Parser/Cigar.pm blib/lib/Bio/Tradis/Parser/Cigar.pm
cp lib/Bio/Tradis/RemoveTags.pm blib/lib/Bio/Tradis/RemoveTags.pm
cp lib/Bio/Tradis/CommandLine/RunMapping.pm blib/lib/Bio/Tradis/CommandLine/RunMapping.pm
cp lib/Bio/Tradis/DetectTags.pm blib/lib/Bio/Tradis/DetectTags.pm
cp lib/Bio/Tradis/CommandLine/TradisAnalysis.pm blib/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm
cp lib/Bio/Tradis/CommandLine/FilterFastqTags.pm blib/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm
cp lib/Bio/Tradis/TradisPlot.pm blib/lib/Bio/Tradis/TradisPlot.pm
cp lib/Bio/Tradis/CommandLine/CheckTags.pm blib/lib/Bio/Tradis/CommandLine/CheckTags.pm
cp lib/Bio/Tradis/CombinePlots.pm blib/lib/Bio/Tradis/CombinePlots.pm
cp lib/Bio/Tradis/CommandLine/AddTags.pm blib/lib/Bio/Tradis/CommandLine/AddTags.pm
cp lib/Bio/Tradis/Samtools.pm blib/lib/Bio/Tradis/Samtools.pm
cp lib/Bio/Tradis/RunTradis.pm blib/lib/Bio/Tradis/RunTradis.pm
cp lib/Bio/Tradis/AddTagsToSeq.pm blib/lib/Bio/Tradis/AddTagsToSeq.pm
cp lib/Bio/Tradis/Parser/Fastq.pm blib/lib/Bio/Tradis/Parser/Fastq.pm
cp lib/Bio/Tradis/FilterTags.pm blib/lib/Bio/Tradis/FilterTags.pm
cp lib/Bio/Tradis/Map.pm blib/lib/Bio/Tradis/Map.pm
cp lib/Bio/Tradis/Exception.pm blib/lib/Bio/Tradis/Exception.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
cp bin/filter_tradis_tags blib/script/filter_tradis_tags
"/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/remove_tradis_tags blib/script/remove_tradis_tags
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/filter_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
cp bin/tradis_essentiality.R 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_comparison.R
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_essentiality.R
"/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]: Leaving directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
dh_auto_test || true
make -j11 test TEST_VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/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 7.70
#
# === Build Requires ===
#
# Module Want Have
# ------------------- ---- ----
# ExtUtils::MakeMaker any 7.70
#
# === Test Requires ===
#
# Module Want Have
# ------------------- ---- --------
# Env::Path 0.18 0.19
# ExtUtils::MakeMaker any 7.70
# File::Spec any 3.90
# Test::Exception any 0.43
# Test::Files any 0.26
# Test::More any 1.302199
# Test::Most any 0.38
#
# === Test Recommends ===
#
# Module Want Have
# ---------- -------- --------
# CPAN::Meta 2.120900 2.150010
#
# === Runtime Requires ===
#
# Module Want Have
# ---------------- ---- ------
# Bio::Seq any 1.7.8
# Bio::SeqIO any 1.7.8
# Cwd any 3.90
# Data::Dumper any 2.189
# Exception::Class any 1.45
# File::Basename any 2.86
# File::Path any 2.18
# File::Spec any 3.90
# File::Temp any 0.2311
# FindBin any 1.54
# Getopt::Long any 2.57
# Moose any 2.2207
# Text::CSV any 2.04
# Try::Tiny any 0.32
# strict any 1.13
# warnings any 1.70
#
t/00-report-prereqs.t ......................
1..1
ok 1
ok
# Failed test 'checking file contents'
# at /usr/share/perl5/Test/Files.pm line 376.
# --- t/data/output.sam
# +++ t/data/AddTags/expected_tradis.sam
# @@ -15,9 +15,7 @@
# @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'
# @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
# @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
# -@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -H t/data/AddTags/sample_sm_tr.bam
# -@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -h -S -b -o t/data/output.bam tmp.20241218035320.sam
# -@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h -o t/data/output.sam t/data/output.bam
# +@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.bam
# 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
# 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
# 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 /usr/share/perl5/Test/Files.pm line 376.
# --- t/data/AddTags/sample_sm_no_tr.sam
# +++ t/data/output.sam
# @@ -15,7 +15,9 @@
# @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'
# @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
# @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
# -@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -h -o t/data/AddTags/sample_sm_no_tr.sam t/data/AddTags/sample_sm_no_tr.bam
# +@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -H t/data/AddTags/sample_sm_tr.bam
# +@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -h -S -b -o t/data/output.bam tmp.20241218035320.sam
# +@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h -o t/data/output.sam t/data/output.bam
# 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
# 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
# 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": Destination address required
[E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta : No such file or directory
[E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta'
[W::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": Destination address required
[E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta : No such file or directory
[E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta'
[W::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": Destination address required
[E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta : No such file or directory
[E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta'
[W::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 /usr/share/perl5/Test/Files.pm line 376.
# --- t/data/output.sam
# +++ t/data/AddTags/expected_tradis.sam
# @@ -1,4 +1,6 @@
# @HD VN:1.4 SO:coordinate
# +@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
# +@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
# @PG ID:SCS PN:MiSeq Control Software DS:Controlling software on instrument VN:2.2.0
# @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.28.0
# @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
# @@ -13,8 +15,4 @@
# @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'
# @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
# @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
# -@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -H t/data/AddTags/sample_sm_tr.cram
# +@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.cram
# -@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -h -S -C -o t/data/output.cram tmp.20241218035320.sam
# -@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h -o t/data/output.sam t/data/output.cram
# -@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
# -@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
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[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(0x5903e44c) 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(0x57fe1234)') called at lib/Bio/Tradis/CommandLine/TradisAnalysis.pm line 146
Bio::Tradis::CommandLine::TradisAnalysis::run('Bio::Tradis::CommandLine::TradisAnalysis=HASH(0x57fe1234)') 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
Attempt to call undefined import method with arguments ("") via package "Bio::Tradis::Parser::Bam" (Perhaps you forgot to load the package?) at lib/Bio/Tradis/DetectTags.pm line 9.
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Destination address required
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
# Failed test 'checking mapped file contents'
# at /usr/share/perl5/Test/Files.pm line 376.
# --- /build/reproducible-path/bio-tradis-1.4.5+dfsg2/tmp_run_tradis_tests_PqyMv/tmp1.sam
# +++ /build/reproducible-path/bio-tradis-1.4.5+dfsg2/tmp_run_tradis_tests_PqyMv/tmp2.sam
# @@ -1,5 +1,4 @@
# @SQ SN:AE004091 LN:9840
# -@HD VN:1.5 SO:unsorted GO:query
# HS21_09876:1:1105:9650:48712#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0
# HS21_09876:1:1106:8638:38957#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0
# HS21_09876:1:1204:19746:42237#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0
# Looks like you failed 1 test of 45.
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
not 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
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/45 subtests
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
# Failed test 'checking mapped file contents'
# at /usr/share/perl5/Test/Files.pm line 376.
# --- /build/reproducible-path/bio-tradis-1.4.5+dfsg2/tmp_run_tradis_tagless_tests_ePyu8/tmp1.sam
# +++ /build/reproducible-path/bio-tradis-1.4.5+dfsg2/tmp_run_tradis_tagless_tests_ePyu8/tmp2.sam
# @@ -1,5 +1,4 @@
# @SQ SN:AE004091 LN:9840
# -@HD VN:1.5 SO:unsorted GO:query
# HS21_09876:1:1105:9650:48712#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0
# HS21_09876:1:1106:8638:38957#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0
# HS21_09876:1:1204:19746:42237#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0
# Looks like you failed 1 test of 22.
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
not 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
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/22 subtests
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 (exited 3) Tests: 15 Failed: 3)
Failed tests: 6, 9, 15
Non-zero exit status: 3
t/Bio/Tradis/CommandLine/TradisAnalysis.t (Wstat: 65280 (exited 255) Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/Bio/Tradis/RunTradisBWA.t (Wstat: 256 (exited 1) Tests: 45 Failed: 1)
Failed test: 18
Non-zero exit status: 1
t/Bio/Tradis/RunTradisTaglessBwa.t (Wstat: 256 (exited 1) Tests: 22 Failed: 1)
Failed test: 5
Non-zero exit status: 1
Files=18, Tests=309, 12 wallclock secs ( 0.10 usr 0.04 sys + 9.36 cusr 1.98 csys = 11.48 CPU)
Result: FAIL
Failed 4/18 test programs. 5/309 subtests failed.
make[2]: *** [Makefile:1077: test_dynamic] Error 255
make[2]: Leaving directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
dh_auto_test: error: make -j11 test TEST_VERBOSE=1 returned exit code 2
make[1]: Leaving directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/bio-tradis/
make -j11 install DESTDIR=/build/reproducible-path/bio-tradis-1.4.5\+dfsg2/debian/bio-tradis AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[1]: Entering directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
Manifying 9 pod documents
Manifying 25 pod documents
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/RemoveTags.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/RunTradis.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Exception.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/DetectTags.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/FilterTags.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Map.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/TradisPlot.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CombinePlots.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Samtools.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/AddTagsToSeq.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Fastq.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Bam.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Cigar.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisBam.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/CheckTags.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RunMapping.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotCombine.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotTradis.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RemoveFastqTags.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisAnalysis.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/FilterFastqTags.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/AddTags.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/InsertSite.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/Exceptions.pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/filter_tradis_tags.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/add_tradis_tags.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/check_tradis_tags.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/tradis_plot.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/remove_tradis_tags.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/tradis_gene_insert_sites.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/bacteria_tradis.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man1/combine_tradis_plots.1p
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::AddTags.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotCombine.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::TradisPlot.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Samtools.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::Exceptions.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RemoveTags.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Fastq.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::InsertSite.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisBam.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::CheckTags.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::DetectTags.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::AddTagsToSeq.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Map.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Bam.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Cigar.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::FilterTags.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RemoveFastqTags.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotTradis.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisAnalysis.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CombinePlots.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RunMapping.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::FilterFastqTags.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Exception.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RunTradis.3pm
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/bacteria_tradis
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/add_tradis_tags
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/remove_tradis_tags
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_comparison.R
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_merge_plots
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_plot
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_essentiality.R
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/combine_tradis_plots
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/tradis_gene_insert_sites
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/check_tradis_tags
Installing /build/reproducible-path/bio-tradis-1.4.5+dfsg2/debian/bio-tradis/usr/bin/filter_tradis_tags
make[1]: Leaving directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/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]: Leaving directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/bio-tradis-1.4.5+dfsg2'
dh_installman
rm debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p*
make[1]: Leaving directory '/build/reproducible-path/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: building package 'bio-tradis' in '../bio-tradis_1.4.5+dfsg2-2_all.deb'.
dpkg-genbuildinfo --build=binary -O../bio-tradis_1.4.5+dfsg2-2_i386.buildinfo
dpkg-genchanges --build=binary -O../bio-tradis_1.4.5+dfsg2-2_i386.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: not including original source code in upload
I: copying local configuration
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/27270 and its subdirectories
I: Current time: Tue Dec 17 15:53:37 -12 2024
I: pbuilder-time-stamp: 1734494017