I: pbuilder: network access will be disabled during build I: Current time: Sun May 17 03:23:03 +14 2020 I: pbuilder-time-stamp: 1589635383 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [art-nextgen-simulation-tools_20160605+dfsg-3.dsc] I: copying [./art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz] I: copying [./art-nextgen-simulation-tools_20160605+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Jul 29 19:47:00 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./art-nextgen-simulation-tools_20160605+dfsg-3.dsc 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-3.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10278/tmp/hooks/D01_modify_environment starting debug: Running on profitbricks-build2-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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/10278/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/10278/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=5ae0cc76d36a4b22897553ad54697cc0 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=10278 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.vBKJlxzv67/pbuilderrc_EUDL --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.vBKJlxzv67/b2 --logfile b2/build.log art-nextgen-simulation-tools_20160605+dfsg-3.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://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-9-686-pae #1 SMP Debian 4.19.118-2 (2020-04-29) i686 GNU/Linux I: ls -l /bin total 5496 -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash -rwxr-xr-x 1 root root 120676 Mar 1 2019 date -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd -rwxr-xr-x 1 root root 100620 Mar 1 2019 df -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 34532 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln -rwxr-xr-x 1 root root 55400 Jul 27 2018 login -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 10 2019 more -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 May 17 03:28 sh -> bash lrwxrwxrwx 1 root root 4 May 15 22:26 sh.distrib -> dash -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty -rwsr-xr-x 1 root root 71072 Jan 10 2019 su -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch -rwxr-xr-x 1 root root 34532 Mar 1 2019 true -rwxr-xr-x 1 root root 17768 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/10278/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 (>= 11~), 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 ... 19234 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgsl-dev{a} libgsl23{a} libgslcblas0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{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 libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 21.4 MB of archives. After unpacking 79.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libgslcblas0 i386 2.5+dfsg-6 [99.2 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libgsl23 i386 2.5+dfsg-6 [855 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libgsl-dev i386 2.5+dfsg-6 [1076 kB] Fetched 21.4 MB in 11s (1871 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... 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I: Building the package 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 dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build 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-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.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 stdbool.h that conforms to C99... yes checking for _Bool... 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 configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j10 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: 0.289938 The random seed for the run: 1589635840 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: 0.190703 The random seed for the run: 1589635846 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: 0.236477 The random seed for the run: 1589635850 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: 35.5773 The random seed for the run: 1589635855 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: 20.1491 The random seed for the run: 1589636158 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: 0.164745 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: 0.132801 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: 0.274859 The random seed for the run: 1589636215 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: 0.40289 The random seed for the run: 1589636216 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: 0.465527 The random seed for the run: 1589636217 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: 0.225993 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: 0.254501 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: 0.680044 The random seed for the run: 1589636218 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: 695.118 The random seed for the run: 1589636219 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: 457.59 The random seed for the run: 1589638251 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: 283.07 The random seed for the run: 1589640004 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: 0.1574 The random seed for the run: 1589641001 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: 0.116455 The random seed for the run: 1589641001 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: 0.088051 The random seed for the run: 1589641002 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: 0.162997 The random seed for the run: 1589641003 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: 0.17736 The random seed for the run: 1589641006 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: 1.33828 The random seed for the run: 1589641009 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: 1.05352 The random seed for the run: 1589641042 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: 0.937142 The random seed for the run: 1589641065 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: 0.07254 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: 0.072594 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: 0.084835 The random seed for the run: 1589641069 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: 0.076382 The random seed for the run: 1589641069 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 fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j10 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'. /bin/mkdir -p '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /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_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/art-nextgen-simulation-tools/usr/bin/art_illumina debian/art-nextgen-simulation-tools/usr/bin/art_454 debian/art-nextgen-simulation-tools/usr/bin/art_SOLiD were not linked against libgslcblas.so.0 (they use none of the library's symbols) 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-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-3_i386.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-3_i386.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../art-nextgen-simulation-tools_20160605+dfsg-3_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) I: copying local configuration I: user script /srv/workspace/pbuilder/10278/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/10278/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/10278 and its subdirectories I: Current time: Sun May 17 04:58:24 +14 2020 I: pbuilder-time-stamp: 1589641104