Diff of the two buildlogs:
--
--- b1/build.log 2025-03-06 14:04:51.614997246 +0000
+++ b2/build.log 2025-03-06 14:08:10.966005693 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Wed Apr 8 08:26:18 -12 2026
-I: pbuilder-time-stamp: 1775679978
+I: Current time: Fri Mar 7 04:04:54 +14 2025
+I: pbuilder-time-stamp: 1741269894
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
@@ -24,52 +24,84 @@
dpkg-source: info: applying reproducible.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/3108647/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/4059932/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos11-amd64.
+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 Mar 6 14:05 /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/4059932/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/4059932/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build/reproducible-path'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='amd64'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
- DISTRIBUTION='unstable'
- HOME='/root'
- HOST_ARCH='amd64'
+ 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=amd64
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
+ DIRSTACK=()
+ DISTRIBUTION=unstable
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=x86_64
+ HOST_ARCH=amd64
IFS='
'
- INVOCATION_ID='5abf6dbb48764988a3816f10a7364855'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- MAIL='/var/mail/root'
- OPTIND='1'
- PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
- PBCURRENTCOMMANDLINEOPERATION='build'
- PBUILDER_OPERATION='build'
- PBUILDER_PKGDATADIR='/usr/share/pbuilder'
- PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
- PBUILDER_SYSCONFDIR='/etc'
- PPID='3108647'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=0468f29260e14c1eb9033b0c9cac4f36
+ LANG=C
+ LANGUAGE=et_EE:et
+ LC_ALL=C
+ MACHTYPE=x86_64-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=4059932
PS4='+ '
- PWD='/'
- SHELL='/bin/bash'
- SHLVL='2'
- SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Brf15s5A/pbuilderrc_xCP5 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Brf15s5A/b1 --logfile b1/build.log samtools_1.21-1.dsc'
- SUDO_GID='110'
- SUDO_UID='105'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://213.165.73.152:3128'
+ 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.Brf15s5A/pbuilderrc_aDqi --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Brf15s5A/b2 --logfile b2/build.log samtools_1.21-1.dsc'
+ SUDO_GID=111
+ SUDO_UID=106
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://46.16.76.132:3128
I: uname -a
- Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/3108647/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/4059932/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -227,7 +259,7 @@
Get: 98 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-1 [105 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-1 [353 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB]
-Fetched 42.1 MB in 6s (7147 kB/s)
+Fetched 42.1 MB in 1s (56.8 MB/s)
Preconfiguring packages ...
Selecting previously unselected package autoconf-archive.
(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 ... 19783 files and directories currently installed.)
@@ -642,7 +674,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/samtools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../samtools_1.21-1_source.changes
+I: user script /srv/workspace/pbuilder/4059932/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/4059932/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/samtools-1.21/ && 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 > ../samtools_1.21-1_source.changes
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.21-1
dpkg-buildpackage: info: source distribution unstable
@@ -657,7 +693,7 @@
rm -f config.mk
touch config.mk
dh_auto_clean --
- make -j42 distclean
+ make -j20 distclean
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai
@@ -744,7 +780,7 @@
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
- make -j42 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
+ make -j20 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
@@ -762,140 +798,140 @@
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
-echo '#define SAMTOOLS_VERSION "1.21"' > version.h
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
+echo '#define SAMTOOLS_VERSION "1.21"' > version.h
+cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
echo '#define SAMTOOLS_CC "gcc"' >> version.h
cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
+echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h
+echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"' >> version.h
+echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h
+echo '#define SAMTOOLS_HTSDIR ""' >> version.h
+echo '#define SAMTOOLS_LIBS ""' >> version.h
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h
+sed -i -e 's@/build/reproducible-path/samtools-1.21@�BUILDPATH�@g' version.h
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c
+cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c
-echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"' >> version.h
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
-echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
-echo '#define SAMTOOLS_HTSDIR ""' >> version.h
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
-echo '#define SAMTOOLS_LIBS ""' >> version.h
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
-echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
-sed -i -e 's@/build/reproducible-path/samtools-1.21@�BUILDPATH�@g' version.h
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c
-cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c
-cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c
-cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
-cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz
-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz
+gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
+gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz
cc1: warning: command-line option '-frelease' is valid for D but not for C
-cc1: warning: command-line option '-frelease' is valid for D but not for C
-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz
+gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread
-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread
+gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread
gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
@@ -913,7 +949,7 @@
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
dh_auto_test -- BGZIP=/usr/bin/bgzip
- make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip
+ make -j20 test "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
test/split/test_count_rg
test/split/test_expand_format_string
@@ -952,75 +988,75 @@
/build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/4EwtYsZSfJ/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/84salXSzJ4/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/4EwtYsZSfJ/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/84salXSzJ4/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/4EwtYsZSfJ/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/84salXSzJ4/bgzip.dat.gz
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa 3:11-13 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa.gz 3:11-13 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa 2:998-1003 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa 1:100-104 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa.gz 1:100-104 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa 1:99998-100007 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools faidx /tmp/4EwtYsZSfJ/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/build/reproducible-path/samtools-1.21/samtools faidx /tmp/84salXSzJ4/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq 3:11-13
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq 3:11-13
.. ok
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq.gz 3:11-13
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq.gz 3:11-13
.. ok
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq 2:998-1003
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq 2:998-1003
.. ok
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq.gz 2:998-1003
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq.gz 2:998-1003
.. ok
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq 1:100-104
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq 1:100-104
.. ok
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq.gz 1:100-104
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq.gz 1:100-104
.. ok
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq 1:99998-100007
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq 1:99998-100007
.. ok
.. ok
-/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/4EwtYsZSfJ/fqidx.fq.gz 1:99998-100007
+/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/84salXSzJ4/fqidx.fq.gz 1:99998-100007
.. ok
.. ok
@@ -1030,7 +1066,7 @@
.. ok
test_dict:
- /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/4EwtYsZSfJ/dict.fa.gz
+ /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/84salXSzJ4/dict.fa.gz
.. ok
test_dict:
@@ -1046,11 +1082,11 @@
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view /tmp/4EwtYsZSfJ/large_chrom.bam ref2
+ /build/reproducible-path/samtools-1.21/samtools view /tmp/84salXSzJ4/large_chrom.bam ref2
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view /tmp/4EwtYsZSfJ/large_chrom.bam ref2:1-541556283
+ /build/reproducible-path/samtools-1.21/samtools view /tmp/84salXSzJ4/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -1058,19 +1094,19 @@
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/4EwtYsZSfJ/test_input_1_b.bam.bai ref2
+ /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/84salXSzJ4/test_input_1_b.bam.bai ref2
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/4EwtYsZSfJ/test_input_1_b.bam.bai
+ /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/84salXSzJ4/test_input_1_b.bam.bai
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/4EwtYsZSfJ/test_input_1_b.bam.bai
+ /build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/84salXSzJ4/test_input_1_b.bam.bai
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/4EwtYsZSfJ/test_input_1_b_opt.bam.bai ref2
+ /build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/84salXSzJ4/test_input_1_b_opt.bam.bai ref2
.. ok
test_index:
@@ -1086,23 +1122,23 @@
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/4EwtYsZSfJ/auto_indexed.csi && cat /tmp/4EwtYsZSfJ/auto_indexed.csi
+ /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/84salXSzJ4/auto_indexed.csi && cat /tmp/84salXSzJ4/auto_indexed.csi
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/4EwtYsZSfJ/auto_indexed.crai && cat /tmp/4EwtYsZSfJ/auto_indexed.crai
+ /build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/84salXSzJ4/auto_indexed.crai && cat /tmp/84salXSzJ4/auto_indexed.crai
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/4EwtYsZSfJ/auto_indexed.csi && cat /tmp/4EwtYsZSfJ/auto_indexed.csi
+ /build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/84salXSzJ4/auto_indexed.csi && cat /tmp/84salXSzJ4/auto_indexed.csi
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/4EwtYsZSfJ/large_chrom.bam ref2
+ /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/84salXSzJ4/large_chrom.bam ref2
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/4EwtYsZSfJ/large_chrom.bam ref2:1-541556283
+ /build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/84salXSzJ4/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -1110,19 +1146,19 @@
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/4EwtYsZSfJ/test_input_1_b.bam.bai ref2
+ /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/84salXSzJ4/test_input_1_b.bam.bai ref2
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/4EwtYsZSfJ/test_input_1_b.bam.bai
+ /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/84salXSzJ4/test_input_1_b.bam.bai
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/4EwtYsZSfJ/test_input_1_b.bam.bai
+ /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/84salXSzJ4/test_input_1_b.bam.bai
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/4EwtYsZSfJ/test_input_1_b_opt.bam.bai ref2
+ /build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/84salXSzJ4/test_input_1_b_opt.bam.bai ref2
.. ok
test_index:
@@ -1138,39 +1174,39 @@
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/4EwtYsZSfJ/auto_indexed.csi && cat /tmp/4EwtYsZSfJ/auto_indexed.csi
+ /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/84salXSzJ4/auto_indexed.csi && cat /tmp/84salXSzJ4/auto_indexed.csi
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/4EwtYsZSfJ/auto_indexed.crai && cat /tmp/4EwtYsZSfJ/auto_indexed.crai
+ /build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/84salXSzJ4/auto_indexed.crai && cat /tmp/84salXSzJ4/auto_indexed.crai
.. ok
test_index:
- /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/4EwtYsZSfJ/auto_indexed.csi && cat /tmp/4EwtYsZSfJ/auto_indexed.csi
+ /build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/84salXSzJ4/auto_indexed.csi && cat /tmp/84salXSzJ4/auto_indexed.csi
.. ok
test_mpileup:
- /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/4EwtYsZSfJ/mpileup.bam.list -f /tmp/4EwtYsZSfJ/mpileup.ref.fa.gz -r17:100-150
+ /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/84salXSzJ4/mpileup.bam.list -f /tmp/84salXSzJ4/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/4EwtYsZSfJ/mpileup.cram.list -f /tmp/4EwtYsZSfJ/mpileup.ref.fa.gz -r17:100-150
+ /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/84salXSzJ4/mpileup.cram.list -f /tmp/84salXSzJ4/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/4EwtYsZSfJ/mpileup.bam.urllist -f /tmp/4EwtYsZSfJ/mpileup.ref.fa.gz -r17:100-150
+ /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/84salXSzJ4/mpileup.bam.urllist -f /tmp/84salXSzJ4/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/4EwtYsZSfJ/mpileup.cram.urllist -f /tmp/4EwtYsZSfJ/mpileup.ref.fa.gz -r17:100-150
+ /build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/84salXSzJ4/mpileup.cram.urllist -f /tmp/84salXSzJ4/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/4EwtYsZSfJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/4EwtYsZSfJ/mpileup.1.bam | grep -v mpileup
+ /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/84salXSzJ4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/84salXSzJ4/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/4EwtYsZSfJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/4EwtYsZSfJ/mpileup.1.cram | grep -v mpileup
+ /build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/84salXSzJ4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/84salXSzJ4/mpileup.1.cram | grep -v mpileup
.. ok
test_mpileup:
@@ -1458,53 +1494,53 @@
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/4EwtYsZSfJ/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/84salXSzJ4/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/4EwtYsZSfJ/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/84salXSzJ4/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/4EwtYsZSfJ/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/84salXSzJ4/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/4EwtYsZSfJ/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/84salXSzJ4/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/4EwtYsZSfJ/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/84salXSzJ4/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/4EwtYsZSfJ/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/84salXSzJ4/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/4EwtYsZSfJ/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/84salXSzJ4/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/4EwtYsZSfJ/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/84salXSzJ4/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/4EwtYsZSfJ/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/84salXSzJ4/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/4EwtYsZSfJ/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/84salXSzJ4/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/4EwtYsZSfJ/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/84salXSzJ4/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/4EwtYsZSfJ/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/84salXSzJ4/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/4EwtYsZSfJ/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/84salXSzJ4/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/4EwtYsZSfJ/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/84salXSzJ4/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/4EwtYsZSfJ/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/84salXSzJ4/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/4EwtYsZSfJ/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/84salXSzJ4/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/4EwtYsZSfJ/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/84salXSzJ4/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/4EwtYsZSfJ/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/84salXSzJ4/view.001.fogn (CRAM input).. ok
- 67: Filter -N /tmp/4EwtYsZSfJ/view.001.forn (SAM input) .. ok
+ 67: Filter -N /tmp/84salXSzJ4/view.001.forn (SAM input) .. ok
- 68: Count -N /tmp/4EwtYsZSfJ/view.001.forn (SAM input) .. ok
+ 68: Count -N /tmp/84salXSzJ4/view.001.forn (SAM input) .. ok
- 69: Filter -N /tmp/4EwtYsZSfJ/view.001.forn (BAM input) .. ok
+ 69: Filter -N /tmp/84salXSzJ4/view.001.forn (BAM input) .. ok
- 70: Count -N /tmp/4EwtYsZSfJ/view.001.forn (BAM input) .. ok
+ 70: Count -N /tmp/84salXSzJ4/view.001.forn (BAM input) .. ok
- 71: Filter -N /tmp/4EwtYsZSfJ/view.001.forn (CRAM input) .. ok
+ 71: Filter -N /tmp/84salXSzJ4/view.001.forn (CRAM input) .. ok
- 72: Count -N /tmp/4EwtYsZSfJ/view.001.forn (CRAM input) .. ok
+ 72: Count -N /tmp/84salXSzJ4/view.001.forn (CRAM input) .. ok
73: Filter -d BC (SAM input) .. ok
@@ -1530,53 +1566,53 @@
84: Count -d BC:TGCA (CRAM input) .. ok
- 85: Filter -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (SAM input) .. ok
+ 85: Filter -D BC:/tmp/84salXSzJ4/view.001.fobc (SAM input) .. ok
- 86: Count -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (SAM input) .. ok
+ 86: Count -D BC:/tmp/84salXSzJ4/view.001.fobc (SAM input) .. ok
- 87: Filter -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (BAM input) .. ok
+ 87: Filter -D BC:/tmp/84salXSzJ4/view.001.fobc (BAM input) .. ok
- 88: Count -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (BAM input) .. ok
+ 88: Count -D BC:/tmp/84salXSzJ4/view.001.fobc (BAM input) .. ok
- 89: Filter -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (CRAM input) .. ok
+ 89: Filter -D BC:/tmp/84salXSzJ4/view.001.fobc (CRAM input) .. ok
- 90: Count -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (CRAM input) .. ok
+ 90: Count -D BC:/tmp/84salXSzJ4/view.001.fobc (CRAM input) .. ok
- 91: Filter -D BC:/tmp/4EwtYsZSfJ/view.001.fobc -d BC:TGCA (SAM input).. ok
+ 91: Filter -D BC:/tmp/84salXSzJ4/view.001.fobc -d BC:TGCA (SAM input).. ok
- 92: Count -D BC:/tmp/4EwtYsZSfJ/view.001.fobc -d BC:TGCA (SAM input).. ok
+ 92: Count -D BC:/tmp/84salXSzJ4/view.001.fobc -d BC:TGCA (SAM input).. ok
- 93: Filter -D BC:/tmp/4EwtYsZSfJ/view.001.fobc -d BC:TGCA (BAM input).. ok
+ 93: Filter -D BC:/tmp/84salXSzJ4/view.001.fobc -d BC:TGCA (BAM input).. ok
- 94: Count -D BC:/tmp/4EwtYsZSfJ/view.001.fobc -d BC:TGCA (BAM input).. ok
+ 94: Count -D BC:/tmp/84salXSzJ4/view.001.fobc -d BC:TGCA (BAM input).. ok
- 95: Filter -D BC:/tmp/4EwtYsZSfJ/view.001.fobc -d BC:TGCA (CRAM input).. ok
+ 95: Filter -D BC:/tmp/84salXSzJ4/view.001.fobc -d BC:TGCA (CRAM input).. ok
- 96: Count -D BC:/tmp/4EwtYsZSfJ/view.001.fobc -d BC:TGCA (CRAM input).. ok
+ 96: Count -D BC:/tmp/84salXSzJ4/view.001.fobc -d BC:TGCA (CRAM input).. ok
- 97: Filter -d BC:TGCA -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (SAM input).. ok
+ 97: Filter -d BC:TGCA -D BC:/tmp/84salXSzJ4/view.001.fobc (SAM input).. ok
- 98: Count -d BC:TGCA -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (SAM input).. ok
+ 98: Count -d BC:TGCA -D BC:/tmp/84salXSzJ4/view.001.fobc (SAM input).. ok
- 99: Filter -d BC:TGCA -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (BAM input).. ok
+ 99: Filter -d BC:TGCA -D BC:/tmp/84salXSzJ4/view.001.fobc (BAM input).. ok
- 100: Count -d BC:TGCA -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (BAM input).. ok
+ 100: Count -d BC:TGCA -D BC:/tmp/84salXSzJ4/view.001.fobc (BAM input).. ok
- 101: Filter -d BC:TGCA -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (CRAM input).. ok
+ 101: Filter -d BC:TGCA -D BC:/tmp/84salXSzJ4/view.001.fobc (CRAM input).. ok
- 102: Count -d BC:TGCA -D BC:/tmp/4EwtYsZSfJ/view.001.fobc (CRAM input).. ok
+ 102: Count -d BC:TGCA -D BC:/tmp/84salXSzJ4/view.001.fobc (CRAM input).. ok
- 103: Filter -D RG:/tmp/4EwtYsZSfJ/view.001.fogn (SAM input) .. ok
+ 103: Filter -D RG:/tmp/84salXSzJ4/view.001.fogn (SAM input) .. ok
- 104: Count -D RG:/tmp/4EwtYsZSfJ/view.001.fogn (SAM input) .. ok
+ 104: Count -D RG:/tmp/84salXSzJ4/view.001.fogn (SAM input) .. ok
- 105: Filter -D RG:/tmp/4EwtYsZSfJ/view.001.fogn (BAM input) .. ok
+ 105: Filter -D RG:/tmp/84salXSzJ4/view.001.fogn (BAM input) .. ok
- 106: Count -D RG:/tmp/4EwtYsZSfJ/view.001.fogn (BAM input) .. ok
+ 106: Count -D RG:/tmp/84salXSzJ4/view.001.fogn (BAM input) .. ok
- 107: Filter -D RG:/tmp/4EwtYsZSfJ/view.001.fogn (CRAM input).. ok
+ 107: Filter -D RG:/tmp/84salXSzJ4/view.001.fogn (CRAM input).. ok
- 108: Count -D RG:/tmp/4EwtYsZSfJ/view.001.fogn (CRAM input) .. ok
+ 108: Count -D RG:/tmp/84salXSzJ4/view.001.fogn (CRAM input) .. ok
109: Filter -d NE:TGCA (SAM input) .. ok
@@ -1592,126 +1628,126 @@
115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test115.sam -h -d TGCA /tmp/4EwtYsZSfJ/view.001.sam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test115.sam -h -d TGCA /tmp/84salXSzJ4/view.001.sam --no-PG
.. expected failure
116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/4EwtYsZSfJ/view.001.sam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/84salXSzJ4/view.001.sam --no-PG
.. expected failure
117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test117.sam -h -d TGCA /tmp/4EwtYsZSfJ/view.test001.bam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test117.sam -h -d TGCA /tmp/84salXSzJ4/view.test001.bam --no-PG
.. expected failure
118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/4EwtYsZSfJ/view.test001.bam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/84salXSzJ4/view.test001.bam --no-PG
.. expected failure
119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test119.sam -h -d TGCA /tmp/4EwtYsZSfJ/view.test006.cram --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test119.sam -h -d TGCA /tmp/84salXSzJ4/view.test006.cram --no-PG
.. expected failure
120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/4EwtYsZSfJ/view.test006.cram --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/84salXSzJ4/view.test006.cram --no-PG
.. expected failure
- 121: Filter -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/4EwtYsZSfJ/view.001.fobc"
+ 121: Filter -D BClong:/tmp/84salXSzJ4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/84salXSzJ4/view.001.fobc"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test121.sam -h -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc /tmp/4EwtYsZSfJ/view.001.sam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test121.sam -h -D BClong:/tmp/84salXSzJ4/view.001.fobc /tmp/84salXSzJ4/view.001.sam --no-PG
.. expected failure
- 122: Count -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/4EwtYsZSfJ/view.001.fobc"
+ 122: Count -D BClong:/tmp/84salXSzJ4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/84salXSzJ4/view.001.fobc"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc /tmp/4EwtYsZSfJ/view.001.sam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/84salXSzJ4/view.001.fobc /tmp/84salXSzJ4/view.001.sam --no-PG
.. expected failure
- 123: Filter -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/4EwtYsZSfJ/view.001.fobc"
+ 123: Filter -D BClong:/tmp/84salXSzJ4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/84salXSzJ4/view.001.fobc"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test123.sam -h -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc /tmp/4EwtYsZSfJ/view.test001.bam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test123.sam -h -D BClong:/tmp/84salXSzJ4/view.001.fobc /tmp/84salXSzJ4/view.test001.bam --no-PG
.. expected failure
- 124: Count -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/4EwtYsZSfJ/view.001.fobc"
+ 124: Count -D BClong:/tmp/84salXSzJ4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/84salXSzJ4/view.001.fobc"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc /tmp/4EwtYsZSfJ/view.test001.bam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/84salXSzJ4/view.001.fobc /tmp/84salXSzJ4/view.test001.bam --no-PG
.. expected failure
- 125: Filter -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/4EwtYsZSfJ/view.001.fobc"
+ 125: Filter -D BClong:/tmp/84salXSzJ4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/84salXSzJ4/view.001.fobc"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test125.sam -h -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc /tmp/4EwtYsZSfJ/view.test006.cram --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test125.sam -h -D BClong:/tmp/84salXSzJ4/view.001.fobc /tmp/84salXSzJ4/view.test006.cram --no-PG
.. expected failure
- 126: Count -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/4EwtYsZSfJ/view.001.fobc"
+ 126: Count -D BClong:/tmp/84salXSzJ4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/84salXSzJ4/view.001.fobc"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/4EwtYsZSfJ/view.001.fobc /tmp/4EwtYsZSfJ/view.test006.cram --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/84salXSzJ4/view.001.fobc /tmp/84salXSzJ4/view.test006.cram --no-PG
.. expected failure
127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/4EwtYsZSfJ/view.001.sam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/84salXSzJ4/view.001.sam --no-PG
.. expected failure
128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/4EwtYsZSfJ/view.001.sam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/84salXSzJ4/view.001.sam --no-PG
.. expected failure
129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/4EwtYsZSfJ/view.test001.bam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/84salXSzJ4/view.test001.bam --no-PG
.. expected failure
130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/4EwtYsZSfJ/view.test001.bam --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/84salXSzJ4/view.test001.bam --no-PG
.. expected failure
131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -o /tmp/4EwtYsZSfJ/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/4EwtYsZSfJ/view.test006.cram --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -o /tmp/84salXSzJ4/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/84salXSzJ4/view.test006.cram --no-PG
.. expected failure
132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2"
Failed command:
- /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/4EwtYsZSfJ/view.test006.cram --no-PG
+ /build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/84salXSzJ4/view.test006.cram --no-PG
.. expected failure
@@ -2613,7 +2649,7 @@
.. ok
test_bam2fq:
- /build/reproducible-path/samtools-1.21/samtools fastq -N -s /tmp/4EwtYsZSfJ/bam2fq.discard.s.fq -0 /tmp/4EwtYsZSfJ/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
+ /build/reproducible-path/samtools-1.21/samtools fastq -N -s /tmp/84salXSzJ4/bam2fq.discard.s.fq -0 /tmp/84salXSzJ4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
@@ -2754,7 +2790,7 @@
.. ok
test_bam2fq:
- /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/4EwtYsZSfJ/bam2fq.discard.s.fq -0 /tmp/4EwtYsZSfJ/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
+ /build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/84salXSzJ4/bam2fq.discard.s.fq -0 /tmp/84salXSzJ4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
@@ -2971,7 +3007,7 @@
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/MbQo266ybL - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
+ /build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/IS6U22WSLt - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -2995,11 +3031,11 @@
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/4EwtYsZSfJ/merge.tag.1.bam /tmp/4EwtYsZSfJ/merge.tag.2.bam
+ /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/84salXSzJ4/merge.tag.1.bam /tmp/84salXSzJ4/merge.tag.2.bam
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/4EwtYsZSfJ/merge.tag.3.bam /tmp/4EwtYsZSfJ/merge.tag.4.bam
+ /build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/84salXSzJ4/merge.tag.3.bam /tmp/84salXSzJ4/merge.tag.4.bam
.. ok
test_merge:
@@ -3007,7 +3043,7 @@
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/4EwtYsZSfJ/merge.bed.1.bam /tmp/4EwtYsZSfJ/merge.bed.2.bam
+ /build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/84salXSzJ4/merge.bed.1.bam /tmp/84salXSzJ4/merge.bed.2.bam
.. ok
test_merge:
@@ -3027,7 +3063,7 @@
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/i_whategXI - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
+ /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/v2JwRhlftp - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -3051,11 +3087,11 @@
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/4EwtYsZSfJ/merge.tag.1.bam /tmp/4EwtYsZSfJ/merge.tag.2.bam
+ /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/84salXSzJ4/merge.tag.1.bam /tmp/84salXSzJ4/merge.tag.2.bam
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/4EwtYsZSfJ/merge.tag.3.bam /tmp/4EwtYsZSfJ/merge.tag.4.bam
+ /build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/84salXSzJ4/merge.tag.3.bam /tmp/84salXSzJ4/merge.tag.4.bam
.. ok
test_merge:
@@ -3063,7 +3099,7 @@
.. ok
test_merge:
- /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/4EwtYsZSfJ/merge.bed.1.bam /tmp/4EwtYsZSfJ/merge.bed.2.bam
+ /build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/84salXSzJ4/merge.bed.1.bam /tmp/84salXSzJ4/merge.bed.2.bam
.. ok
test_merge:
@@ -3075,15 +3111,15 @@
.. ok
test_sort:
- /build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/4EwtYsZSfJ/sortout
+ /build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/84salXSzJ4/sortout
.. ok
test_sort:
- /build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/4EwtYsZSfJ/sortout.bam
+ /build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/84salXSzJ4/sortout.bam
.. ok
test_sort:
- /build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/4EwtYsZSfJ/sorttmp
+ /build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/84salXSzJ4/sorttmp
.. ok
test_sort:
@@ -3135,15 +3171,15 @@
.. ok
test_sort:
- /build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/4EwtYsZSfJ/sortout
+ /build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/84salXSzJ4/sortout
.. ok
test_sort:
- /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/4EwtYsZSfJ/sortout.bam
+ /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/84salXSzJ4/sortout.bam
.. ok
test_sort:
- /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/4EwtYsZSfJ/sorttmp
+ /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/84salXSzJ4/sorttmp
.. ok
test_sort:
@@ -3847,15 +3883,15 @@
.. ok
test_large_positions:
- /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/4EwtYsZSfJ/longref.sam.gz
+ /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/84salXSzJ4/longref.sam.gz
.. ok
test_large_positions:
- /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/4EwtYsZSfJ/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
+ /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/84salXSzJ4/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok
test_large_positions:
- /build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/4EwtYsZSfJ/longref.sam.gz
+ /build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/84salXSzJ4/longref.sam.gz
.. ok
test_large_positions:
@@ -3875,7 +3911,7 @@
.. ok
test_large_positions:
- /build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/4EwtYsZSfJ/longref.sam.gz
+ /build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/84salXSzJ4/longref.sam.gz
.. ok
test_large_positions:
@@ -4123,7 +4159,7 @@
Unexpected failures: 0
=> PASS
make[2]: Leaving directory '/build/reproducible-path/samtools-1.21'
- rm -fr -- /tmp/dh-xdg-rundir-6o2PpNRC
+ rm -fr -- /tmp/dh-xdg-rundir-1r8rBX9U
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
create-stamp debian/debhelper-build-stamp
dh_prep
@@ -4135,7 +4171,7 @@
dh_auto_install -- \
prefix=/usr
install -m0755 -d /build/reproducible-path/samtools-1.21/debian/tmp
- make -j42 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
+ make -j20 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
mkdir -p -m 755 /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1
install -p samtools /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin
@@ -4220,93 +4256,79 @@
dh_installman
rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1
- man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
+ man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1
man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/wgsim.1
- mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
- mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
+ mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1
+ mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1
+ mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1
+ mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1
+ mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1
+ mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1
mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1
chmod 0644 -- debian/samtools/usr/share/man/man1/wgsim.1
- mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1
- mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1
- mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1
- mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1
mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1
mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1
+ mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1
mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1
+ mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1
+ mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1
+ mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1
+ mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
+ mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1
mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1
mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1
- mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1
- mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1
+ mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1
mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1
mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1
- mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1
- mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1
- mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1
- mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1
+ mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1
+ mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1
+ mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1
mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1
mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1
- mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1
- mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1
- mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1
- mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1
- mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1
- mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1
- mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1
- mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1
mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1
- mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1
+ mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1
mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1
mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1
- mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1
+ mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
+ mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1
+ mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1
+ mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1
+ mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1
+ mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1
+ mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1
+ mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1
+ mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-idxstats.1 debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1
mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1
- mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1
- mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1
mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1
mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1
- mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1
- mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1
- chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1
+ chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1
dh_lintian
install -m0755 -d debian/samtools/usr/share/lintian/overrides
install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
@@ -4336,8 +4358,8 @@
find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
@@ -4355,41 +4377,41 @@
objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug
chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug
dh_strip -a
- install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67
- objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/715784ea360047a454fd2afe166174780413f5.debug
- chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/715784ea360047a454fd2afe166174780413f5.debug
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
- objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/715784ea360047a454fd2afe166174780413f5.debug debian/samtools/usr/bin/md5fa
- install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1
- objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/b93a5fa5ac7c9b18631e9aeef56642e58fdb83.debug
- chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/b93a5fa5ac7c9b18631e9aeef56642e58fdb83.debug
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
- objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/b93a5fa5ac7c9b18631e9aeef56642e58fdb83.debug debian/samtools/usr/bin/md5sum-lite
- install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1
- objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/1130721ac7f4e6af5c5f3b1079cc6183f9ce39.debug
- chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/1130721ac7f4e6af5c5f3b1079cc6183f9ce39.debug
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
- objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/1130721ac7f4e6af5c5f3b1079cc6183f9ce39.debug debian/samtools/usr/bin/maq2sam-long
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/55
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/55/f655233a865e19999ce957d7e6444d3523107f.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/55/f655233a865e19999ce957d7e6444d3523107f.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/55/f655233a865e19999ce957d7e6444d3523107f.debug debian/samtools/usr/bin/ace2sam
- install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4
- objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/afd142edcb947fd1c225686de6ab3f9fced6b4.debug
- chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/afd142edcb947fd1c225686de6ab3f9fced6b4.debug
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
- objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/afd142edcb947fd1c225686de6ab3f9fced6b4.debug debian/samtools/usr/bin/wgsim
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/93
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/93/7d7ec187599dec615b6f6a38a04f5b42d6dc2a.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/93/7d7ec187599dec615b6f6a38a04f5b42d6dc2a.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/93/7d7ec187599dec615b6f6a38a04f5b42d6dc2a.debug debian/samtools/usr/bin/samtools
+ install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/b93a5fa5ac7c9b18631e9aeef56642e58fdb83.debug
+ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/b93a5fa5ac7c9b18631e9aeef56642e58fdb83.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/b93a5fa5ac7c9b18631e9aeef56642e58fdb83.debug debian/samtools/usr/bin/md5sum-lite
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/fcb83fdbf9b863ecf820436512b880a1128f92.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/fcb83fdbf9b863ecf820436512b880a1128f92.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/fcb83fdbf9b863ecf820436512b880a1128f92.debug debian/samtools/usr/bin/maq2sam-short
+ install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/715784ea360047a454fd2afe166174780413f5.debug
+ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/715784ea360047a454fd2afe166174780413f5.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/715784ea360047a454fd2afe166174780413f5.debug debian/samtools/usr/bin/md5fa
+ install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/1130721ac7f4e6af5c5f3b1079cc6183f9ce39.debug
+ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/1130721ac7f4e6af5c5f3b1079cc6183f9ce39.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b1/1130721ac7f4e6af5c5f3b1079cc6183f9ce39.debug debian/samtools/usr/bin/maq2sam-long
+ install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/afd142edcb947fd1c225686de6ab3f9fced6b4.debug
+ chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/afd142edcb947fd1c225686de6ab3f9fced6b4.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/afd142edcb947fd1c225686de6ab3f9fced6b4.debug debian/samtools/usr/bin/wgsim
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/samtools/usr/lib/debug/.dwz
@@ -4401,30 +4423,30 @@
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/samtools/DEBIAN
- dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim
dh_installdeb
install -m0755 -d debian/samtools/DEBIAN
install -m0755 -d debian/samtools-test/DEBIAN
dh_gencontrol
- install -m0755 -d debian/samtools-test/DEBIAN
- echo misc:Depends= >> debian/samtools-test.substvars
- echo misc:Pre-Depends= >> debian/samtools-test.substvars
- dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test
install -m0755 -d debian/samtools/DEBIAN
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=46fcb83fdbf9b863ecf820436512b880a1128f92 55f655233a865e19999ce957d7e6444d3523107f 67715784ea360047a454fd2afe166174780413f5 937d7ec187599dec615b6f6a38a04f5b42d6dc2a a1b93a5fa5ac7c9b18631e9aeef56642e58fdb83 b11130721ac7f4e6af5c5f3b1079cc6183f9ce39 e4afd142edcb947fd1c225686de6ab3f9fced6b4" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
+ install -m0755 -d debian/samtools-test/DEBIAN
+ echo misc:Depends= >> debian/samtools-test.substvars
+ echo misc:Pre-Depends= >> debian/samtools-test.substvars
+ dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test
+dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined
+ chmod 0644 -- debian/samtools-test/DEBIAN/control
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools
-dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined
- chmod 0644 -- debian/samtools-test/DEBIAN/control
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
chmod 0644 -- debian/samtools/DEBIAN/control
dh_md5sums
- install -m0755 -d debian/samtools-test/DEBIAN
install -m0755 -d debian/samtools/DEBIAN
+ install -m0755 -d debian/samtools-test/DEBIAN
cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/samtools/DEBIAN/md5sums
@@ -4434,11 +4456,11 @@
chmod 0644 -- debian/samtools-test/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/samtools ..
- dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/samtools-test ..
-dpkg-deb: building package 'samtools' in '../samtools_1.21-1_amd64.deb'.
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.21-1_amd64.deb'.
+ dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools-test' in '../samtools-test_1.21-1_all.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.21-1_amd64.deb'.
+dpkg-deb: building package 'samtools' in '../samtools_1.21-1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../samtools_1.21-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../samtools_1.21-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -4447,12 +4469,14 @@
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/4059932/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/4059932/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/3108647 and its subdirectories
-I: Current time: Wed Apr 8 08:27:50 -12 2026
-I: pbuilder-time-stamp: 1775680070
+I: removing directory /srv/workspace/pbuilder/4059932 and its subdirectories
+I: Current time: Fri Mar 7 04:08:10 +14 2025
+I: pbuilder-time-stamp: 1741270090