I: pbuilder: network access will be disabled during build I: Current time: Fri Jun 14 22:16:14 +14 2024 I: pbuilder-time-stamp: 1718352974 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [art-nextgen-simulation-tools_20160605+dfsg-4.dsc] I: copying [./art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz] I: copying [./art-nextgen-simulation-tools_20160605+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 23 22:24:58 2020 +14 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 ./art-nextgen-simulation-tools_20160605+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting art-nextgen-simulation-tools in art-nextgen-simulation-tools-20160605+dfsg dpkg-source: info: unpacking art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz dpkg-source: info: unpacking art-nextgen-simulation-tools_20160605+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-test-comparison.patch dpkg-source: info: applying adapt_path_to_perl_scripts.patch dpkg-source: info: applying spellings.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/124444/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. 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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 14 22:16 /bin/sh -> /bin/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/124444/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/124444/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=4130dd2de18f42eaa00467f48e699525 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=124444 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/r-b-build.s5JN7kXa/pbuilderrc_EXTQ --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.s5JN7kXa/b2 --logfile b2/build.log --extrapackages usrmerge art-nextgen-simulation-tools_20160605+dfsg-4.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 2023 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 2023 more -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 Jun 14 22:16 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 2023 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/124444/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 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), libgsl-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 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 libgsl-dev; however: Package libgsl-dev 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After unpacking 82.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libgslcblas0 i386 2.7.1+dfsg-3+b1 [107 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libgsl27 i386 2.7.1+dfsg-3+b1 [929 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libgsl-dev i386 2.7.1+dfsg-3+b1 [1176 kB] Fetched 21.2 MB in 2s (11.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19604 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgslcblas0:i386. Preparing to unpack .../30-libgslcblas0_2.7.1+dfsg-3+b1_i386.deb ... Unpacking libgslcblas0:i386 (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libgsl27:i386. Preparing to unpack .../31-libgsl27_2.7.1+dfsg-3+b1_i386.deb ... Unpacking libgsl27:i386 (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../32-libgsl-dev_2.7.1+dfsg-3+b1_i386.deb ... Unpacking libgsl-dev (2.7.1+dfsg-3+b1) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libicu72:i386 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libgslcblas0:i386 (2.7.1+dfsg-3+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:i386 (2.7.1+dfsg-3+b1) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libgsl-dev (2.7.1+dfsg-3+b1) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/124444/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/124444/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/art-nextgen-simulation-tools-20160605+dfsg/ && 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 > ../art-nextgen-simulation-tools_20160605+dfsg-4_source.changes dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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 configure.ac:8: installing './compile' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' Makefile.am: installing './INSTALL' Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for main in -lm... yes checking for main in -lgslcblas... yes checking for main in -lgsl... yes checking whether make sets $(MAKE)... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for size_t... yes checking for floor... yes checking for pow... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j15 make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' make all-am make[2]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/art_illumina.o art_illumina_src/art_illumina.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/art_qual_scale.o art_illumina_src/art_qual_scale.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/empdist.o art_illumina_src/empdist.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/readSeqFile.o art_illumina_src/readSeqFile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/seqRead.o art_illumina_src/seqRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_illumina_src/samRead.o art_illumina_src/samRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/art_454.o art_454_src/art_454.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/art.o art_454_src/art.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/read_profile.o art_454_src/read_profile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/readSeqFile.o art_454_src/readSeqFile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/seqRead.o art_454_src/seqRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_454_src/samRead.o art_454_src/samRead.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/art_SOLiD.o art_SOLiD_src/art_SOLiD.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/art.o art_SOLiD_src/art.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/readSeqFile.o art_SOLiD_src/readSeqFile.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/read_SOLiD.o art_SOLiD_src/read_SOLiD.cpp g++ -DHAVE_CONFIG_H -I. -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o art_SOLiD_src/samRead.o art_SOLiD_src/samRead.cpp g++ -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o art_454 art_454_src/art_454.o art_454_src/art.o art_454_src/read_profile.o art_454_src/readSeqFile.o art_454_src/seqRead.o art_454_src/samRead.o -lgsl -lgslcblas -lm g++ -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o art_SOLiD art_SOLiD_src/art_SOLiD.o art_SOLiD_src/art.o art_SOLiD_src/readSeqFile.o art_SOLiD_src/read_SOLiD.o art_SOLiD_src/samRead.o -lgsl -lgslcblas -lm g++ -g -O2 -ffile-prefix-map=/build/art-nextgen-simulation-tools-20160605+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o art_illumina art_illumina_src/art_illumina.o art_illumina_src/art_qual_scale.o art_illumina_src/empdist.o art_illumina_src/readSeqFile.o art_illumina_src/seqRead.o art_illumina_src/samRead.o -lgsl -lgslcblas -lm make[2]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' set -e && \ cd examples && \ ./run_test_examples_454.sh && \ ./run_test_examples_SOLiD.sh && \ ./run_test_examples_illumina.sh =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Single-end simulation Total CPU time used: 0.067988 The random seed for the run: 1718353002 Parameters Settings number of flow cycles: 100 fold of read coverage: 10X 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./single_454_flx.fq ALN Alignment File: ./single_454_flx.aln SAM Alignment File: ./single_454_flx.sam Read Coverage File: ./single_454_flx.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Paired-end simulation Total CPU time used: 0.051387 The random seed for the run: 1718353002 Parameters Settings number of flow cycles: 100 fold of read coverage: 5X fragment length mean: 500 std: 20 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence Files: the 1st reads: ./paired_454_flx1.fq the 2nd reads: ./paired_454_flx2.fq ALN Alignment Files: the 1st reads: ./paired_454_flx1.aln the 2nd reads: ./paired_454_flx2.aln SAM Alignment File: ./paired_454_flx.sam Read Coverage File: ./paired_454_flx.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Paired-end simulation Total CPU time used: 0.05569 The random seed for the run: 1718353002 Parameters Settings number of flow cycles: 200 fold of read coverage: 6X fragment length mean: 500 std: 20 454 Profile for Simulation the built-in GS-FLX Titanium profile Output Files FASTQ Sequence Files: the 1st reads: ./paired_454_flxTitan1.fq the 2nd reads: ./paired_454_flxTitan2.fq ALN Alignment Files: the 1st reads: ./paired_454_flxTitan1.aln the 2nd reads: ./paired_454_flxTitan2.aln SAM Alignment File: ./paired_454_flxTitan.sam Read Coverage File: ./paired_454_flxTitan.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Amplicon 5'-end sequencing with single-end reads Total CPU time used: 11.5698 The random seed for the run: 1718353002 Parameters Settings number of flow cycles: 100 # reads per amplion: 10 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./amp_single_454.fq ALN Alignment File: ./amp_single_454.aln SAM Alignment File: ./amp_single_454.sam Read Coverage File: ./amp_single_454.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Amplicon two-end sequencing with paired-end reads Total CPU time used: 9.12264 The random seed for the run: 1718353014 Parameters Settings number of flow cycles: 100 # read pairs per amplion: 5 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence Files: the 1st reads: ./amp_paired_454.fq the 2nd reads: ./amp_paired_4542.fq ALN Alignment Files: the 1st reads: ./amp_paired_454.aln the 2nd reads: ./amp_paired_4542.aln SAM Alignment File: ./amp_paired_454.sam Read Coverage File: ./amp_paired_454.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Single-end simulation Total CPU time used: 0.065384 The random seed for the run: 777 Parameters Settings number of flow cycles: 100 fold of read coverage: 10X 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./single_454_t1.fq ALN Alignment File: ./single_454_t1.aln SAM Alignment File: ./single_454_t1.sam Read Coverage File: ./single_454_t1.stat =================================================================== ART_454 (Version 2.6.0) Simulation of 454 Pyrosequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. =================================================================== Single-end simulation Total CPU time used: 0.066005 The random seed for the run: 777 Parameters Settings number of flow cycles: 100 fold of read coverage: 10X 454 Profile for Simulation the built-in GS-FLX profile Output Files FASTQ Sequence File: ./single_454_t2.fq ALN Alignment File: ./single_454_t2.aln SAM Alignment File: ./single_454_t2.sam Read Coverage File: ./single_454_t2.stat compare difference of two simulation datasets after normalising known difference ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Single-end simulation Total CPU time used: 0.119594 The random seed for the run: 1718353026 Parameters Settings fold of read coverage: 10X read length: 25 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence File: ./single_dat.fq MAP Alignment File: ./single_dat.map SAM Alignment File: ./single_dat.sam convert a map file to a UCSC BED file ../map2bed.pl single_dat.bed single_dat.map ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Single-end simulation Total CPU time used: 0.155213 The random seed for the run: 1718353026 Parameters Settings fold of read coverage: 20X read length: 75 SOLiD Error Profile for Simulation the profile provided: ../SOLiD_profiles/profile_pseudo Output Files FASTQ Sequence File: ./dat_userProfile.fq MAP Alignment File: ./dat_userProfile.map SAM Alignment File: ./dat_userProfile.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Mate-Pair (F3-R3) simulation Total CPU time used: 0.208454 The random seed for the run: 1718353026 Parameters Settings fold of read coverage: 20X F3 read length: 35 R3 read length: 35 fragment length mean: 2000 std: 50 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence Files: the 1st reads: ./matepair_dat_R3.fq the 2nd reads: ./matepair_dat_F3.fq MAP Alignment Files: the 1st reads: ./matepair_dat_R3.map the 2nd reads: ./matepair_dat_F3.map SAM Alignment File: ./matepair_dat.sam convert two map files to a UCSC BED file ../map2bed.pl maptepair.bed matepair_dat1.map matepair_dat2.map ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Mate-Pair (F3-R3) simulation Total CPU time used: 0.098825 The random seed for the run: 777 Parameters Settings fold of read coverage: 10X F3 read length: 50 R3 read length: 50 fragment length mean: 1500 std: 50 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./matepair_fs1_R3.fq the 2nd reads: ./matepair_fs1_F3.fq MAP Alignment Files: the 1st reads: ./matepair_fs1_R3.map the 2nd reads: ./matepair_fs1_F3.map SAM Alignment File: ./matepair_fs1.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Mate-Pair (F3-R3) simulation Total CPU time used: 0.097825 The random seed for the run: 777 Parameters Settings fold of read coverage: 10X F3 read length: 50 R3 read length: 50 fragment length mean: 1500 std: 50 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./matepair_fs2_R3.fq the 2nd reads: ./matepair_fs2_F3.fq MAP Alignment Files: the 1st reads: ./matepair_fs2_R3.map the 2nd reads: ./matepair_fs2_F3.map SAM Alignment File: ./matepair_fs2.sam compare two simulation datasets 4c4 < @PG ID:03 PN:ART_SOLiD CL:../art_SOLiD -r 777 -s testSeq.fa ./matepair_fs1 50 10 1500 50 --- > @PG ID:03 PN:ART_SOLiD CL:../art_SOLiD -r 777 -s testSeq.fa ./matepair_fs2 50 10 1500 50 ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Paired-end (F3-F5) simulation Total CPU time used: 0.317693 The random seed for the run: 1718353027 Parameters Settings fold of read coverage: 50X F3 read length: 75 F5 read length: 35 fragment length mean: 250 std: 10 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./paired_dat_F5.fq the 2nd reads: ./paired_dat_F3.fq MAP Alignment Files: the 1st reads: ./paired_dat_F5.map the 2nd reads: ./paired_dat_F3.map SAM Alignment File: ./paired_dat.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Amplicon single-end sequencing simulation Total CPU time used: 301.31 The random seed for the run: 1718353027 Parameters Settings # reads per amplion: 100 read length: 25 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence File: ./amp_single.fq MAP Alignment File: ./amp_single.map SAM Alignment File: ./amp_single.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Warning: you are using the 75bp error profile for testing only. Amplicon matepair sequencing simulation Total CPU time used: 179.005 The random seed for the run: 1718353338 Parameters Settings # read pairs per amplion: 80 F3 read length: 50 R3 read length: 50 SOLiD Error Profile for Simulation the 75bp error profile for testing only Output Files FASTQ Sequence Files: the 1st reads: ./amp_matepair_R3.fq the 2nd reads: ./amp_matepair_F3.fq MAP Alignment Files: the 1st reads: ./amp_matepair_R3.map the 2nd reads: ./amp_matepair_F3.map SAM Alignment File: ./amp_matepair.sam ================================================================= ART_SOLiD (Version 1.3.3) Simulation of Applied Biosystems' SOLiD Sequencing Copyright (c) 2008-2015, Weichun Huang. All Rights Reserved. ================================================================= Amplicon paired-end sequencing simulation Total CPU time used: 114.948 The random seed for the run: 1718353518 Parameters Settings # read pairs per amplion: 50 F3 read length: 35 F5 read length: 25 SOLiD Error Profile for Simulation the built-in 35bp error profile Output Files FASTQ Sequence Files: the 1st reads: ./amp_paired_F5.fq the 2nd reads: ./amp_paired_F3.fq MAP Alignment Files: the 1st reads: ./amp_paired_F5.map the 2nd reads: ./amp_paired_F3.map SAM Alignment File: ./amp_paired.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Single-end Simulation Total CPU time used: 0.062683 The random seed for the run: 1718353639 Parameters used during run Read Length: 35 Genome masking 'N' cutoff frequency: 1 in 35 Fold Coverage: 10X Profile Type: Combined ID Tag: Quality Profile(s) First Read: Genome Analyzer I Length 36 R1 (built-in profile) Output files FASTQ Sequence File: ./single_end_com.fq ALN Alignment File: ./single_end_com.aln SAM Alignment File: ./single_end_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Single-end Simulation Total CPU time used: 0.048996 The random seed for the run: 1718353639 Parameters used during run Read Length: 50 Genome masking 'N' cutoff frequency: 1 in 50 Fold Coverage: 10X Profile Type: Separated ID Tag: Quality Profile(s) First Read: MiniSeq TruSeq Length 51 R1 (built-in profile) Output files FASTQ Sequence File: ./single_end_sep.fq ALN Alignment File: ./single_end_sep.aln SAM Alignment File: ./single_end_sep.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.031022 The random seed for the run: 1718353639 Parameters used during run Read Length: 150 Genome masking 'N' cutoff frequency: 1 in 150 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeq 2500 Length 150 R1 (built-in profile) First Read: HiSeq 2500 Length 150 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com1.fq the 2nd reads: ./paired_end_com2.fq ALN Alignment Files: the 1st reads: ./paired_end_com1.aln the 2nd reads: ./paired_end_com2.aln SAM Alignment File: ./paired_end_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.050735 The random seed for the run: 1718353639 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Separated ID Tag: Quality Profile(s) First Read: HiSeq 2000 Length 100 R1 (built-in profile) First Read: HiSeq 2000 Length 100 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_sep1.fq the 2nd reads: ./paired_end_sep2.fq ALN Alignment Files: the 1st reads: ./paired_end_sep1.aln the 2nd reads: ./paired_end_sep2.aln SAM Alignment File: ./paired_end_sep.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Matepair-end sequencing simulation Total CPU time used: 0.037071 The random seed for the run: 1718353639 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 2500 Standard Deviation: 50 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeq 2500 Length 126 R1 (built-in profile) First Read: HiSeq 2500 Length 126 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./matepair_com1.fq the 2nd reads: ./matepair_com2.fq ALN Alignment Files: the 1st reads: ./matepair_com1.aln the 2nd reads: ./matepair_com2.aln SAM Alignment File: ./matepair_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon 5'-end sequencing simulation Total CPU time used: 0.386797 The random seed for the run: 1718353639 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Reads per Amplion: 2 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeqX v2.5 TruSeq Length 151 R1 (built-in profile) Output files FASTQ Sequence File: ./amp_5_end_com.fq ALN Alignment File: ./amp_5_end_com.aln SAM Alignment File: ./amp_5_end_com.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon paired-end sequencing simulation Total CPU time used: 0.430569 The random seed for the run: 1718353639 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Read Pairs per Amplion: 1 Profile Type: Combined ID Tag: Quality Profile(s) First Read: MiSeq v1 Length 250 R1 (built-in profile) First Read: MiSeq v1 Length 250 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./amp_pair1.fq the 2nd reads: ./amp_pair2.fq ALN Alignment Files: the 1st reads: ./amp_pair1.aln the 2nd reads: ./amp_pair2.aln SAM Alignment File: ./amp_pair.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Amplicon matepair sequencing simulation Total CPU time used: 0.562839 The random seed for the run: 1718353640 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 # Read Pairs per Amplion: 1 Profile Type: Combined ID Tag: Quality Profile(s) First Read: MiSeq v3 Length 251 R1 (built-in profile) First Read: MiSeq v3 Length 251 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./amp_matepair1.fq the 2nd reads: ./amp_matepair2.fq ALN Alignment Files: the 1st reads: ./amp_matepair1.aln the 2nd reads: ./amp_matepair2.aln SAM Alignment File: ./amp_matepair.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.035647 The random seed for the run: 777 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com_f11.fq the 2nd reads: ./paired_end_com_f12.fq ALN Alignment Files: the 1st reads: ./paired_end_com_f11.aln the 2nd reads: ./paired_end_com_f12.aln SAM Alignment File: ./paired_end_com_f1.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.034818 The random seed for the run: 777 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeqX v2.5 PCR free Length 151 R1 (built-in profile) First Read: HiSeqX v2.5 PCR free Length 151 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com_f21.fq the 2nd reads: ./paired_end_com_f22.fq ALN Alignment Files: the 1st reads: ./paired_end_com_f21.aln the 2nd reads: ./paired_end_com_f22.aln SAM Alignment File: ./paired_end_com_f2.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.04024 The random seed for the run: 1718353640 Parameters used during run Read Length: 100 Genome masking 'N' cutoff frequency: 1 in 100 Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 First quality shift: 10 Second quality shift: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: HiSeq 2000 Length 100 R1 (built-in profile) First Read: HiSeq 2000 Length 100 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_end_com_f11.fq the 2nd reads: ./paired_end_com_f12.fq ALN Alignment Files: the 1st reads: ./paired_end_com_f11.aln the 2nd reads: ./paired_end_com_f12.aln SAM Alignment File: ./paired_end_com_f1.sam ====================ART==================== ART_Illumina (2008-2016) Q Version 2.5.8 (June 6, 2016) Contact: Weichun Huang ------------------------------------------- Paired-end sequencing simulation Total CPU time used: 0.036083 The random seed for the run: 1718353641 Parameters used during run Read Length: 75 'N' genomic regions masking turned off Fold Coverage: 10X Mean Fragment Length: 500 Standard Deviation: 10 Profile Type: Combined ID Tag: Quality Profile(s) First Read: NextSeq 500 v2 Length 76 R1 (built-in profile) First Read: NextSeq 500 v2 Length 76 R2 (built-in profile) Output files FASTQ Sequence Files: the 1st reads: ./paired_nomask1.fq the 2nd reads: ./paired_nomask2.fq ALN Alignment Files: the 1st reads: ./paired_nomask1.aln the 2nd reads: ./paired_nomask2.aln SAM Alignment File: ./paired_nomask.sam rm -f *.aln *.fq *.bed *.map *.sam *.stat make[1]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j15 install DESTDIR=/build/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c art_illumina art_454 art_SOLiD '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c aln2bed.pl map2bed.pl ART_profiler_454/art_profiler_454 ART_profiler_illumina/combinedAvg.pl ART_profiler_illumina/fastqReadAvg.pl ART_profiler_illumina/art_profiler_illumina ART_profiler_illumina/empDist.pl ART_profiler_illumina/summation.pl '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_install-arch make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' dh_install -a # aln2bed.pl seems to be of general use - the other perl scripts are called by art_profiler_illumina # see patch for the latter regarding PATH to *.pl files mkdir -p debian/art-nextgen-simulation-tools/usr/lib/art-nextgen-simulation-tools for pl in debian/art-nextgen-simulation-tools/usr/bin/*.pl ; do \ if [ `basename ${pl}` = aln2bed.pl ] ; then \ mv ${pl} debian/art-nextgen-simulation-tools/usr/bin/`basename ${pl} .pl` ; \ else \ mv ${pl} debian/art-nextgen-simulation-tools/usr/lib/art-nextgen-simulation-tools ; \ fi ; \ done make[1]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' dh_install -Nart-nextgen-simulation-tools dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' dh_installchangelogs ChangeLog make[1]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_installexamples-arch make[1]: Entering directory '/build/art-nextgen-simulation-tools-20160605+dfsg' dh_installexamples -a for ex in examples/run_test_examples_*.sh ; do \ sed -e 's?=\.\./?=/usr/bin/?' \ -e 's?^\.\./?/usr/bin/?' \ -e 's/aln2bed\.pl/aln2bed/' \ $ex > debian/art-nextgen-simulation-tools/usr/share/doc/art-nextgen-simulation-tools/examples/`basename $ex` ; \ done make[1]: Leaving directory '/build/art-nextgen-simulation-tools-20160605+dfsg' dh_installexamples -Nart-nextgen-simulation-tools dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-4_all.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4_i386.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-4_i386.deb'. dpkg-genbuildinfo --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-4_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: user script /srv/workspace/pbuilder/124444/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/124444/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/124444 and its subdirectories I: Current time: Fri Jun 14 22:27:32 +14 2024 I: pbuilder-time-stamp: 1718353652