Diff of the two buildlogs:
--
--- b1/build.log 2021-08-09 14:06:38.614595156 +0000
+++ b2/build.log 2021-08-09 14:09:35.272032202 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Mon Aug 9 01:47:36 -12 2021
-I: pbuilder-time-stamp: 1628516856
+I: Current time: Mon Sep 12 10:29:41 +14 2022
+I: pbuilder-time-stamp: 1662928181
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz]
I: copying local configuration
@@ -17,7 +17,7 @@
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
-gpgv: Signature made Wed Jul 4 22:10:34 2018 -12
+gpgv: Signature made Fri Jul 6 00:10:34 2018 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
@@ -33,136 +33,170 @@
dpkg-source: info: applying enable_tests_in_local_dir.patch
I: using fakeroot in build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/5957/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/17433/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos15-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
+Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
+Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
+Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
+Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash'
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/17433/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/17433/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build'
- 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=15'
- DISTRIBUTION=''
- HOME='/root'
- HOST_ARCH='amd64'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+ BASH_VERSION='5.0.3(1)-release'
+ BUILDDIR=/build
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=amd64
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
+ DIRSTACK=()
+ DISTRIBUTION=
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=x86_64
+ HOST_ARCH=amd64
IFS='
'
- INVOCATION_ID='a5068db5cf3e4d1695ceef6443903c9e'
- 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='5957'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=f43c625f48c443afa5c191e6aa6f6f42
+ 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=17433
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/tmp.beyfWko9o2/pbuilderrc_qG8Z --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.beyfWko9o2/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-2.dsc'
- SUDO_GID='111'
- SUDO_UID='106'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://78.137.99.97:3128'
+ 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/tmp.beyfWko9o2/pbuilderrc_7pS8 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.beyfWko9o2/b2 --logfile b2/build.log microbiomeutil_20101212+dfsg1-2.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://85.184.249.68:3128
I: uname -a
- Linux ionos11-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) x86_64 GNU/Linux
I: ls -l /bin
total 5116
- -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash
- -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2
- -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff
- -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep
- -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep
- -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep
- -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2
- -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover
- lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore
- -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore
- -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat
- -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp
- -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod
- -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown
- -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp
- -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash
- -rwxr-xr-x 1 root root 109408 Feb 28 2019 date
- -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd
- -rwxr-xr-x 1 root root 93744 Feb 28 2019 df
- -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir
- -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg
- lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname
- lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname
- -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo
- -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep
- -rwxr-xr-x 1 root root 35424 Feb 28 2019 false
- -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep
- -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt
- -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount
- -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep
- -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip
- -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe
- -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip
- -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname
- -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln
- -rwxr-xr-x 1 root root 56760 Jul 26 2018 login
- -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls
- -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk
- -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir
- -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod
- -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp
- -rwxr-xr-x 1 root root 43008 Jan 9 2019 more
- -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount
- -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint
- -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv
- lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname
- lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5
- -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd
- lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash
- -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink
- -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm
- -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir
- -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts
- -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed
- lrwxrwxrwx 1 root root 4 Aug 6 20:24 sh -> dash
- -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep
- -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty
- -rwsr-xr-x 1 root root 63568 Jan 9 2019 su
- -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync
- -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar
- -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile
- -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch
- -rwxr-xr-x 1 root root 35424 Feb 28 2019 true
- -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server
- -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount
- -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname
- -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress
- -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir
- -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl
- -rwxr-xr-x 1 root root 946 Jan 21 2019 which
- lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname
- -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat
- -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp
- -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff
- -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep
- -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep
- -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce
- -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep
- -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless
- -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore
- -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew
-I: user script /srv/workspace/pbuilder/5957/tmp/hooks/D02_print_environment finished
+ -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash
+ -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2
+ -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff
+ -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep
+ -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep
+ -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep
+ -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2
+ -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover
+ lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore
+ -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore
+ -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat
+ -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp
+ -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod
+ -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown
+ -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp
+ -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash
+ -rwxr-xr-x 1 root root 109408 Mar 1 2019 date
+ -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd
+ -rwxr-xr-x 1 root root 93744 Mar 1 2019 df
+ -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir
+ -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname
+ -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo
+ -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep
+ -rwxr-xr-x 1 root root 35424 Mar 1 2019 false
+ -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep
+ -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt
+ -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount
+ -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep
+ -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip
+ -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe
+ -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip
+ -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname
+ -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln
+ -rwxr-xr-x 1 root root 56760 Jul 27 2018 login
+ -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls
+ -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk
+ -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir
+ -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod
+ -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp
+ -rwxr-xr-x 1 root root 43008 Jan 10 2019 more
+ -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount
+ -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint
+ -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname
+ lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5
+ -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd
+ lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash
+ -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink
+ -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm
+ -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir
+ -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts
+ -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed
+ lrwxrwxrwx 1 root root 4 Sep 12 10:29 sh -> bash
+ lrwxrwxrwx 1 root root 4 Sep 10 04:47 sh.distrib -> dash
+ -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep
+ -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty
+ -rwsr-xr-x 1 root root 63568 Jan 10 2019 su
+ -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync
+ -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar
+ -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile
+ -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch
+ -rwxr-xr-x 1 root root 35424 Mar 1 2019 true
+ -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server
+ -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount
+ -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname
+ -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress
+ -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir
+ -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl
+ -rwxr-xr-x 1 root root 946 Jan 22 2019 which
+ lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname
+ -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat
+ -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp
+ -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff
+ -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep
+ -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep
+ -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce
+ -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep
+ -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless
+ -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore
+ -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew
+I: user script /srv/workspace/pbuilder/17433/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -259,7 +293,7 @@
Get: 55 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 56 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB]
Get: 57 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB]
-Fetched 40.1 MB in 3s (12.6 MB/s)
+Fetched 40.1 MB in 1s (62.8 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libbsd0:amd64.
(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 ... 19195 files and directories currently installed.)
@@ -512,7 +546,7 @@
fakeroot is already the newest version (1.23-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
-I: Running cd /build/microbiomeutil-20101212+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
+I: Running cd /build/microbiomeutil-20101212+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b
dpkg-buildpackage: info: source package microbiomeutil
dpkg-buildpackage: info: source version 20101212+dfsg1-2
dpkg-buildpackage: info: source distribution unstable
@@ -524,7 +558,7 @@
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1'
dh_auto_clean
- make -j15 clean
+ make -j16 clean
make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1'
X=`pwd`; \
for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \
@@ -577,7 +611,7 @@
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1'
dh_auto_build
- make -j15 "INSTALL=install --strip-program=true"
+ make -j16 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1'
X=`pwd`; \
for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \
@@ -612,70 +646,64 @@
formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null
-Building a new DB, current time: 08/09/2021 01:50:10
+Building a new DB, current time: 09/12/2022 10:30:07
New DB name: /build/microbiomeutil-20101212+dfsg1/RESOURCES/rRNA16S.gold.fasta
New DB title: RESOURCES/rRNA16S.gold.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
-Adding sequences from FASTA; added 5181 sequences in 2.68771 seconds.
+Adding sequences from FASTA; added 5181 sequences in 0.308747 seconds.
cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta
5181 entries from file RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta were indexed in file RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta.cidx
make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1'
dh_auto_test
- make -j15 test
+ make -j16 test
make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1'
cd NAST-iEr; make test
cd WigeoN; make test
+cd ChimeraSlayer; make test
make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-cd ./sample_data; make test
-cd ChimeraSlayer; make test
make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
+make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer'
+make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
+cd ./sample_data; make test
+cd ./sample_data; make test
cd ./sample_data; make test
make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data'
#
make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data'
+make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data'
+#
#
-make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer'
-make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
-cd ./sample_data; make test
#*************** TESTING NAST-iEr ***********************
+#********** TESTING Chimera Slayer *************"
#************* TESTING WigeoN ********************"
#
#
-make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data'
#
-./testForUtils.pl
./runMe.sh
-#********** TESTING Chimera Slayer *************"
-#
./runMe.sh
+./testForUtils.pl
./runMe.sh
query to NAST format
-../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST
-
-
+../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST\n\n
Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC contains: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/x86_64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ../run_WigeoN.pl line 13.
BEGIN failed--compilation aborted at ../run_WigeoN.pl line 13.
+CMD: ../../ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl --query_NAST chims.NAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta --db_FASTA ../../RESOURCES/rRNA16S.gold.fasta -n 15 -P 90 -R 1.007 > chims.NAST.CPS
make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data'
make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN'
-CMD: ../../ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl --query_NAST chims.NAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta --db_FASTA ../../RESOURCES/rRNA16S.gold.fasta -n 15 -P 90 -R 1.007 > chims.NAST.CPS
query and template (profile) to query NAST and template consensus NAST
-../NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST
-
-
+../NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST\n\n
converting NAST mfasta to multi-alignment output highlighting differences
-../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign
-
-
+../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign\n\n
Run via the megablast wrapper
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
Num template seqs to align to: 2
Alignment parameters:
MATCH: 5
@@ -685,35 +713,35 @@
Highest score: 11681
make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data'
make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr'
-
T(1)=10 s
-ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 10 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=7 s
-ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 7 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=9 s
-ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 9 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=7 s
-ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 7 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=0 s
+ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
+
T(1)=1 s
+ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19249.query --db_NAST /tmp/tmp.19249.db -R 1.007
T(1)=2 s
-ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 2 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=9 s
-ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 9 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=9 s
-ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 9 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=7 s
-ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 7 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=6 s
-ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 6 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.29721.query --db_NAST /tmp/tmp.29721.db -R 1.007
-
T(1)=10 s
-ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 10 seconds
+ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 2 seconds
CMD: ../../ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS_RENAST
processing: ChimeraParentSelector chmraD24_7000004128191580_1-4580:4581-7682_S000428666 YES 100.00[(7000004128191580, NAST:164-4593, ECO:36-940, RawLen:876, G:90.90, L:100.00, 1.100);(S000428666, NAST:4594-6747, ECO:940-1470, RawLen:531, G:84.36, L:100.00, 1.185)]
10 entries from file chims.NAST were indexed in file chims.NAST.cidx
@@ -788,58 +816,58 @@
Highest score: 11227
CMD: ../../ChimeraSlayer/ChimeraPhyloChecker/CPS_to_CPC.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST.CPS_RENAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta -P 90 -R 1.007 --minBS 90 --printAlignments > chims.NAST.CPS.CPC
10 entries from file chims.NAST.CPS_RENAST were indexed in file chims.NAST.CPS_RENAST.cidx
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (7000004128191580, S000428666) or (0, 1) took 27 seconds
-ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 74 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (S000378387, S000016146) or (0, 1) took 27 seconds
-ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 61 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (7000004131500344, S000127669) or (0, 1) took 30 seconds
-ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 57 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (S000004801, S000437365) or (0, 1) took 26 seconds
-ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 56 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (S000437007, S000437299) or (0, 1) took 28 seconds
-ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 52 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (S000414109, S000253432) or (0, 1) took 25 seconds
-ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 56 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (7000004131502379, 7000004128198963) or (0, 1) took 32 seconds
-ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 89 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (S000503167, S000004272) or (0, 1) took 24 seconds
-ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 38 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (S000436014, 7000004128189973) or (0, 1) took 22 seconds
-ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 35 seconds
-/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.64503.query --db_NAST /tmp/tmp.64503.db -P 90 -R 1.007 --minBS 90 --printAlignments
-
examined parents (S000009720, S000437236) or (0, 1) took 24 seconds
-ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 56 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (7000004128191580, S000428666) or (0, 1) took 6 seconds
+ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 13 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (S000378387, S000016146) or (0, 1) took 4 seconds
+ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 10 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (7000004131500344, S000127669) or (0, 1) took 4 seconds
+ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 10 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (S000004801, S000437365) or (0, 1) took 3 seconds
+ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 8 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (S000437007, S000437299) or (0, 1) took 4 seconds
+ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 8 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (S000414109, S000253432) or (0, 1) took 4 seconds
+ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 9 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (7000004131502379, 7000004128198963) or (0, 1) took 5 seconds
+ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 13 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (S000503167, S000004272) or (0, 1) took 3 seconds
+ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 5 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (S000436014, 7000004128189973) or (0, 1) took 3 seconds
+ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 5 seconds
+/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.20235.query --db_NAST /tmp/tmp.20235.db -P 90 -R 1.007 --minBS 90 --printAlignments
+
examined parents (S000009720, S000437236) or (0, 1) took 3 seconds
+ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 8 seconds
CMD: ../../ChimeraSlayer/util/CS_add_taxonomy.pl < chims.NAST.CPS.CPC > chims.NAST.CPS.CPC.wTaxons
CMD: ../../ChimeraSlayer/ChimeraParentSelector/CPC_to_CPS.pl --CPC_output chims.NAST.CPS.CPC --query_NAST chims.NAST.CPS_RENAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS.CPC.align
T(1)=1 s
ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds
-
T(1)=1 s
-ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds
-
T(1)=1 s
-ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds
-
T(1)=1 s
-ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds
+
T(1)=0 s
+ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds
+
T(1)=0 s
+ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds
+
T(1)=0 s
+ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds
T(1)=0 s
ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds
-
T(1)=1 s
-ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds
-
T(1)=1 s
-ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 1 seconds
-
T(1)=1 s
-ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds
+
T(1)=0 s
+ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds
+
T(1)=0 s
+ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds
+
T(1)=0 s
+ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds
T(1)=0 s
ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds
-
T(1)=1 s
-ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 seconds
+
T(1)=0 s
+ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 0 seconds
make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data'
make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer'
make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1'
@@ -888,31 +916,33 @@
dh_shlibdeps
dh_installdeb
dh_gencontrol
-dpkg-gencontrol: warning: package nast-ier: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package wigeon: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package chimeraslayer: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package microbiomeutil-data: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package nast-ier: substitution variable ${perl:Depends} unused, but is defined
+dpkg-gencontrol: warning: package nast-ier: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums
dh_builddeb
-dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-2_all.deb'.
-dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-2_amd64.deb'.
dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-2_all.deb'.
+dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-2_all.deb'.
dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-2_all.deb'.
-dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-2_amd64.deb'.
dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-2_all.deb'.
+dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-2_amd64.deb'.
+dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-2_amd64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../microbiomeutil_20101212+dfsg1-2_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/17433/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/17433/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/5957 and its subdirectories
-I: Current time: Mon Aug 9 02:06:37 -12 2021
-I: pbuilder-time-stamp: 1628517997
+I: removing directory /srv/workspace/pbuilder/17433 and its subdirectories
+I: Current time: Mon Sep 12 10:32:35 +14 2022
+I: pbuilder-time-stamp: 1662928355