I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 12 13:33:26 +14 2024 I: pbuilder-time-stamp: 1720740806 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: 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/9629/tmp/hooks/D01_modify_environment starting debug: Running on codethink11-arm64. 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 Jul 12 13:33 /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/9629/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/9629/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=9629 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.CrOp7DXS/pbuilderrc_GLrC --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.CrOp7DXS/b2 --logfile b2/build.log --extrapackages usrmerge art-nextgen-simulation-tools_20160605+dfsg-4.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jul 10 06:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/9629/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: arm64 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 ... 19611 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 20.3 MB of archives. After unpacking 84.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libgslcblas0 arm64 2.7.1+dfsg-5 [74.8 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libgsl27 arm64 2.7.1+dfsg-5 [817 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libgsl-dev arm64 2.7.1+dfsg-5 [1034 kB] Fetched 20.3 MB in 0s (42.1 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 ... 19611 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_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.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:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.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:arm64. Preparing to unpack .../30-libgslcblas0_2.7.1+dfsg-5_arm64.deb ... Unpacking libgslcblas0:arm64 (2.7.1+dfsg-5) ... Selecting previously unselected package libgsl27:arm64. Preparing to unpack .../31-libgsl27_2.7.1+dfsg-5_arm64.deb ... Unpacking libgsl27:arm64 (2.7.1+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../32-libgsl-dev_2.7.1+dfsg-5_arm64.deb ... Unpacking libgsl-dev (2.7.1+dfsg-5) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libgslcblas0:arm64 (2.7.1+dfsg-5) ... 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:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:arm64 (2.7.1+dfsg-5) ... 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:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (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-5) ... 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/9629/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... I: user script /srv/workspace/pbuilder/9629/tmp/hooks/A99_set_merged_usr finished hostname: Temporary failure in name resolution 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 arm64 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=aarch64-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/aarch64-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 -j8 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_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 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 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: 0.137853 The random seed for the run: 1720740913 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: 0.094078 The random seed for the run: 1720740914 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: 0.111829 The random seed for the run: 1720740914 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: 20.9552 The random seed for the run: 1720740914 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: 14.8491 The random seed for the run: 1720740935 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: 0.134605 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: 0.13624 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: 0.215818 The random seed for the run: 1720740951 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: 0.254598 The random seed for the run: 1720740951 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: 0.324889 The random seed for the run: 1720740951 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: 0.149281 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: 0.152917 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: 0.561785 The random seed for the run: 1720740952 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: 524.746 The random seed for the run: 1720740953 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: 311.367 The random seed for the run: 1720741478 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: 204.064 The random seed for the run: 1720741789 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: 0.115904 The random seed for the run: 1720741993 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: 0.106639 The random seed for the run: 1720741994 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: 0.079886 The random seed for the run: 1720741994 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: 0.137842 The random seed for the run: 1720741994 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: 0.096185 The random seed for the run: 1720741994 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: 0.86061 The random seed for the run: 1720741994 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: 1.11185 The random seed for the run: 1720741995 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: 1.37267 The random seed for the run: 1720741996 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: 0.08414 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: 0.083512 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: 0.1018 The random seed for the run: 1720741998 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: 0.086751 The random seed for the run: 1720741998 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 -j8 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' /usr/bin/mkdir -p '/build/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' 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/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: substitution variable ${perl:Depends} unused, but is defined 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 dh_md5sums dh_builddeb dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-4_arm64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-4_arm64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-4_arm64.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/9629/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/9629/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/9629 and its subdirectories I: Current time: Fri Jul 12 13:53:57 +14 2024 I: pbuilder-time-stamp: 1720742037