Diff of the two buildlogs: -- --- b1/build.log 2023-05-05 16:49:31.831681163 +0000 +++ b2/build.log 2023-05-05 16:58:12.848832799 +0000 @@ -1,6 +1,7 @@ +W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 6 11:10:56 -12 2024 -I: pbuilder-time-stamp: 1717715456 +I: Current time: Sat May 6 06:53:33 +14 2023 +I: pbuilder-time-stamp: 1683305613 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +18,7 @@ I: copying [./gubbins_2.4.1.orig.tar.gz] I: copying [./gubbins_2.4.1-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Feb 13 02:24:30 2022 -12 +gpgv: Signature made Mon Feb 14 04:24:30 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,137 +34,168 @@ dpkg-source: info: applying iqtree2.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23082/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/19165/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 6 06:53 /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/19165/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/19165/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='9adb413faae048e6898c15f3ce7b48da' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='23082' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=19165 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.qhReMFe9/pbuilderrc_31KF --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qhReMFe9/b1 --logfile b1/build.log gubbins_2.4.1-5.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.qhReMFe9/pbuilderrc_flV6 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qhReMFe9/b2 --logfile b2/build.log --extrapackages usrmerge gubbins_2.4.1-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-686-pae #1 SMP Debian 5.10.178-3 (2023-04-22) i686 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 2023 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 2023 more - -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount - -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 2023 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/23082/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more + -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount + -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 6 06:53 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/19165/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -386,7 +418,7 @@ Get: 153 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 python3-wheel all 0.38.4-2 [30.8 kB] Get: 155 http://deb.debian.org/debian bookworm/main i386 raxml i386 8.2.12+dfsg-8+b2 [990 kB] -Fetched 111 MB in 2s (73.7 MB/s) +Fetched 111 MB in 2s (49.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19604 files and directories currently installed.) @@ -1035,8 +1067,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/gubbins-2.4.1/ && 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 > ../gubbins_2.4.1-5_source.changes +I: user script /srv/workspace/pbuilder/19165/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/19165/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/gubbins-2.4.1/ && 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 > ../gubbins_2.4.1-5_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 2.4.1-5 dpkg-buildpackage: info: source distribution unstable @@ -1080,7 +1123,7 @@ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -1101,10 +1144,10 @@ checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -1125,8 +1168,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes @@ -1206,72 +1249,72 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j16 + make -j7 make[1]: Entering directory '/build/gubbins-2.4.1' make all-recursive make[2]: Entering directory '/build/gubbins-2.4.1' Making all in src make[3]: Entering directory '/build/gubbins-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Newickform.lo Newickform.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment_file.lo alignment_file.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o block_tab_file.lo block_tab_file.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o branch_sequences.lo branch_sequences.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o string_cat.lo string_cat.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fasta_of_snp_sites.lo fasta_of_snp_sites.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gff_file.lo gff_file.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gubbins.lo gubbins.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_phylip.lo parse_phylip.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_vcf.lo parse_vcf.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylip_of_snp_sites.lo phylip_of_snp_sites.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqUtil.lo seqUtil.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_searching.lo snp_searching.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites.lo snp_sites.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_statistics.lo tree_statistics.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -fPIC -DPIC -o .libs/branch_sequences.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Newickform.lo Newickform.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment_file.lo alignment_file.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o block_tab_file.lo block_tab_file.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o branch_sequences.lo branch_sequences.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o string_cat.lo string_cat.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong 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gubbins.lo gubbins.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -o gff_file.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_phylip.lo parse_phylip.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_vcf.lo parse_vcf.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -o Newickform.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylip_of_snp_sites.lo phylip_of_snp_sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -o alignment_file.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -o gubbins.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqUtil.lo seqUtil.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_searching.lo snp_searching.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites.lo snp_sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -o gubbins.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_statistics.lo tree_statistics.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_scaling.lo tree_scaling.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -o snp_sites.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -o Newickform.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -o snp_searching.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -o alignment_file.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/i386-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/i386-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm make[3]: Leaving directory '/build/gubbins-2.4.1/src' Making all in release @@ -1285,7 +1328,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/gubbins-2.4.1' dh_auto_test - make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 + make -j7 check "TESTSUITEFLAGS=-j7 --verbose" VERBOSE=1 make[2]: Entering directory '/build/gubbins-2.4.1' Making check in src make[3]: Entering directory '/build/gubbins-2.4.1/src' @@ -1298,7 +1341,6 @@ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c ../tests/helper_methods.c: In function 'compare_files': ../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); @@ -1306,11 +1348,6 @@ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../tests/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays_fn': -../tests/check_branch_sequences.c:67:23: warning: implicit declaration of function 'copy_and_concat_2d_integer_arrays'; did you mean 'copy_and_concat_integer_arrays'? [-Wimplicit-function-declaration] - 67 | output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | copy_and_concat_integer_arrays In file included from ../tests/check_gubbins.c:4: ../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations_fn': ../tests/check_gubbins.c:21:15: warning: implicit declaration of function 'number_of_recombinations_in_file' [-Wimplicit-function-declaration] @@ -1374,10 +1411,16 @@ ../tests/check_snp_sites.c:84:109: warning: too many arguments for format [-Wformat-extra-args] 84 | fail_unless( compare_files("../tests/data/two_sequences.aln.phylip", "two_sequences.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../tests/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays_fn': ../tests/check_snp_sites.c:85:122: warning: too many arguments for format [-Wformat-extra-args] 85 | fail_unless( compare_files("../tests/data/two_sequences.aln.snp_sites.aln","two_sequences.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit +../tests/check_branch_sequences.c:67:23: warning: implicit declaration of function 'copy_and_concat_2d_integer_arrays'; did you mean 'copy_and_concat_integer_arrays'? [-Wimplicit-function-declaration] + 67 | output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | copy_and_concat_integer_arrays +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c +/bin/sh ../libtool --tag=CC --mode=link gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests -g -O2 -ffile-prefix-map=/build/gubbins-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit make[4]: Leaving directory '/build/gubbins-2.4.1/src' make check-TESTS @@ -1421,26 +1464,11 @@ adding license file 'LICENSE.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' running build_ext -test_fasttree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_fasttree_treebuilding_command) ... ok -test_iqtree_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_convert_raw_ancestral_states_to_fasta) ... ok -test_iqtree_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_replace_internal_node_label) ... ok -test_iqtree_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_sequence_reconstruction_command) ... ok -test_iqtree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_treebuilding_command) ... ok -test_raxml_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_convert_raw_ancestral_states_to_fasta) ... ok -test_raxml_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_replace_internal_node_label) ... ok -test_raxml_select_executable_based_on_threads (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_select_executable_based_on_threads) ... ok -test_raxml_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_sequence_reconstruction_command) ... ok -test_raxml_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_treebuilding_command) ... ok -test_check_and_fix_window_size (gubbins.tests.test_utils.TestUtilities.test_check_and_fix_window_size) ... ok -test_delete_files (gubbins.tests.test_utils.TestUtilities.test_delete_files) ... ok -test_do_files_exist (gubbins.tests.test_utils.TestUtilities.test_do_files_exist) ... ok -test_gubbins_command (gubbins.tests.test_utils.TestUtilities.test_gubbins_command) ... ok -test_is_executable (gubbins.tests.test_utils.TestUtilities.test_is_executable) ... ok -test_rename_files (gubbins.tests.test_utils.TestUtilities.test_rename_files) ... ok -test_replace_executable (gubbins.tests.test_utils.TestUtilities.test_replace_executable) ... ok -test_translation_of_filenames_to_final_filenames (gubbins.tests.test_utils.TestUtilities.test_translation_of_filenames_to_final_filenames) ... ok -test_verbose_printer (gubbins.tests.test_utils.TestUtilities.test_verbose_printer) ... ok -test_which (gubbins.tests.test_utils.TestUtilities.test_which) ... ok +test_concatenate_fasta_files (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_concatenate_fasta_files) ... ok +test_get_sequence_names_from_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_get_sequence_names_from_alignment) ... ok +test_number_of_sequences_in_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_number_of_sequences_in_alignment) ... ok +test_reconvert_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_reconvert_fasta_file) ... ok +test_reinsert_gaps_into_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_reinsert_gaps_into_fasta_file) ... ok test_filter_out_removed_taxa_from_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_filter_out_removed_taxa_from_tree) ... ok test_has_tree_been_seen_before (gubbins.tests.test_tree_methods.TestTreeMethods.test_has_tree_been_seen_before) ... ok test_internal_node_taxons_removed_when_used_as_starting_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_internal_node_taxons_removed_when_used_as_starting_tree) ... ok @@ -1457,38 +1485,43 @@ test_root_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_root_tree) ... ok test_split_all_non_bi_nodes (gubbins.tests.test_tree_methods.TestTreeMethods.test_split_all_non_bi_nodes) ... ok test_transfer_internal_node_labels_to_tree (gubbins.tests.test_tree_methods.TestTreeMethods.test_transfer_internal_node_labels_to_tree) ... ok -test_are_all_names_unique (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_are_all_names_unique) ... ok -test_do_the_names_match_the_fasta_file (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_do_the_names_match_the_fasta_file) ... ok -test_is_it_a_valid_newick_tree (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_is_it_a_valid_newick_tree) ... ok -test_concatenate_fasta_files (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_concatenate_fasta_files) ... ok -test_get_sequence_names_from_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_get_sequence_names_from_alignment) ... ok -test_number_of_sequences_in_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_number_of_sequences_in_alignment) ... ok -test_reconvert_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_reconvert_fasta_file) ... ok -test_reinsert_gaps_into_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods.test_reinsert_gaps_into_fasta_file) ... ok +test_fasttree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_fasttree_treebuilding_command) ... ok +test_iqtree_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_convert_raw_ancestral_states_to_fasta) ... ok +test_iqtree_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_replace_internal_node_label) ... ok +test_iqtree_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_sequence_reconstruction_command) ... ok +test_iqtree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_iqtree_treebuilding_command) ... ok +test_raxml_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_convert_raw_ancestral_states_to_fasta) ... ok +test_raxml_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_replace_internal_node_label) ... ok +test_raxml_select_executable_based_on_threads (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_select_executable_based_on_threads) ... ok +test_raxml_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_sequence_reconstruction_command) ... ok +test_raxml_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction.test_raxml_treebuilding_command) ... ok test_dont_filter_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_dont_filter_input_file_with_multiple_duplicate_sequences) ... ok test_filter_out_alignments_with_too_much_missing_data (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_filter_out_alignments_with_too_much_missing_data) ... ok test_input_file_with_all_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_all_duplicate_sequences) ... ok test_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_multiple_duplicate_sequences) ... ok test_input_file_with_no_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_no_duplicate_sequences) ... ok test_input_file_with_one_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta.test_input_file_with_one_duplicate_sequences) ... ok -test_are_all_sequence_names_unique (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_all_sequence_names_unique) ... ok -test_are_all_sequences_the_same_length (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_all_sequences_the_same_length) ... ok -test_are_there_enough_sequences_to_build_a_tree (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_there_enough_sequences_to_build_a_tree) ... ok -test_does_each_sequence_have_a_name (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_does_each_sequence_have_a_name) ... ok -test_does_the_sequence_have_sensible_characters (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_does_the_sequence_have_sensible_characters) ... ok -test_valid_fasta_file (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_valid_fasta_file) ... ok +test_check_and_fix_window_size (gubbins.tests.test_utils.TestUtilities.test_check_and_fix_window_size) ... ok +test_delete_files (gubbins.tests.test_utils.TestUtilities.test_delete_files) ... ok +test_do_files_exist (gubbins.tests.test_utils.TestUtilities.test_do_files_exist) ... ok +test_gubbins_command (gubbins.tests.test_utils.TestUtilities.test_gubbins_command) ... ok +test_is_executable (gubbins.tests.test_utils.TestUtilities.test_is_executable) ... ok +test_rename_files (gubbins.tests.test_utils.TestUtilities.test_rename_files) ... ok +test_replace_executable (gubbins.tests.test_utils.TestUtilities.test_replace_executable) ... ok +test_translation_of_filenames_to_final_filenames (gubbins.tests.test_utils.TestUtilities.test_translation_of_filenames_to_final_filenames) ... ok +test_verbose_printer (gubbins.tests.test_utils.TestUtilities.test_verbose_printer) ... ok +test_which (gubbins.tests.test_utils.TestUtilities.test_which) ... ok test_get_recombination_files (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_get_recombination_files) ... ok test_multiple_files_have_one_match (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_multiple_files_have_one_match) ... ok test_reading_embl_file (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_reading_embl_file) ... ok test_two_files_are_different (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_two_files_are_different) ... ok test_two_files_are_same (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations.test_two_files_are_same) ... ok -test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies.test_cleanup) ... +test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies.test_cleanup) ... ok +test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies.test_fasttree) ... NOTE: gubbins_drawer.py is no longer supported. Instead we recommend using Phandango[1] (http://phandango.net/) to visualise the outputs of Gubbins. [1] James Hadfield, Nicholas J Croucher, Richard J Goater, Khalil Abudahab, David M Aanensen, Simon R Harris. "Phandango: an interactive viewer for bacterial population genomics". Bioinformatics, Volume 34, Issue 2, 15 January 2018, Pages 292–293, https://doi.org/10.1093/bioinformatics/btx610 -Trying multithreaded version of RAxML because no single threaded version of RAxML could be found. Just to warn you, this requires 2 threads. - Your outgroups do not form a clade. Using the first taxon A as the outgroup. Taxon C is in the clade but not in your list of outgroups. @@ -1501,8 +1534,8 @@ Your outgroups do not form a clade. Using the first taxon A as the outgroup. Taxon E is in the clade but not in your list of outgroups. -Error with the input starting tree: Is it a valid Newick file? -Error with the input starting tree: Is it a valid Newick file? +Trying multithreaded version of RAxML because no single threaded version of RAxML could be found. Just to warn you, this requires 2 threads. + Sequences in sample1 and sample3 are identical, removing sample1 from analysis Sequences in sample2 and sample4 are identical, removing sample2 from analysis Excluded sequence sample2 because it had 28.571428571428573 percentage missing data while a maximum of 5 is allowed @@ -1516,20 +1549,6 @@ Sequences in sample2 and sample4 are identical, removing sample2 from analysis Sequences in sample1 and sample3 are identical, removing sample1 from analysis Sequences in sample1 and sample3 are identical, removing sample1 from analysis -All sequence names in the fasta file must be unique -Unexpected error: -Error with the input FASTA file: It is in the wrong format so check its an alignment -Unexpected error: -Error with the input FASTA file: It is in the wrong format so check its an alignment -Each sequence must be the same length -Error with input FASTA file: you need more than 3 sequences to build a meaningful tree -Each sequence must have a name and some genomic data -Error with the input FASTA file: One of the sequence names is blank -Error with the input FASTA file: One of the sequence names is blank -Each sequence must have a name and some genomic data -Error with the input FASTA file: One of the sequences contains odd characters, only ACGTNacgtn- are permitted -Error with the input FASTA file: One of the sequences contains odd characters, only ACGTNacgtn- are permitted -Each sequence must have a name and some genomic data --- Gubbins 2.4.1 --- @@ -1539,14 +1558,14 @@ ...done. Run time: 0.00 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Filtering input alignment... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.aln -...done. Run time: 0.02 s +gubbins /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.aln +...done. Run time: 0.03 s Entering the main loop. @@ -1554,109 +1573,107 @@ Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 -...done. Run time: 0.13 s +...done. Run time: 0.21 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.18 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.29 s Reinserting gaps into the alignment... -...done. Run time: 0.19 s +...done. Run time: 0.30 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.20 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.33 s Checking for convergence... -...done. Run time: 0.20 s +...done. Run time: 0.33 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.27 s +...done. Run time: 0.44 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.32 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.52 s Reinserting gaps into the alignment... -...done. Run time: 0.32 s +...done. Run time: 0.52 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.34 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.56 s Checking for convergence... -...done. Run time: 0.34 s +...done. Run time: 0.56 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.51 s +...done. Run time: 0.82 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.64 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.03 s Reinserting gaps into the alignment... -...done. Run time: 0.64 s +...done. Run time: 1.03 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.65 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.06 s Checking for convergence... -...done. Run time: 0.66 s +...done. Run time: 1.07 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 0.88 s +...done. Run time: 1.42 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.93 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.50 s Reinserting gaps into the alignment... -...done. Run time: 0.93 s +...done. Run time: 1.51 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.95 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.54 s Checking for convergence... -...done. Run time: 0.95 s +...done. Run time: 1.55 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... -ok -test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies.test_fasttree) ... ok -test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies.test_hybrid) ... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 1.04 s +raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 +...done. Run time: 1.70 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.09 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.78 s Reinserting gaps into the alignment... -...done. Run time: 1.10 s +...done. Run time: 1.78 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpyebc8s9f/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.11 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpeopr89tv/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.82 s Checking for convergence... -...done. Run time: 1.12 s +...done. Run time: 1.83 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 1.12 s +...finished. Total run time: 1.83 s --- Gubbins 2.4.1 --- @@ -1664,16 +1681,17 @@ Checking dependencies... ...done. Run time: 0.00 s - +ok +test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies.test_hybrid) ... Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Filtering input alignment... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.aln -...done. Run time: 0.01 s +gubbins /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.aln +...done. Run time: 0.02 s Entering the main loop. @@ -1681,98 +1699,98 @@ Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -out multiple_recombinations.iteration_1.tre /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.15 s +...done. Run time: 0.23 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.19 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.31 s Reinserting gaps into the alignment... -...done. Run time: 0.20 s +...done. Run time: 0.31 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.21 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.34 s Checking for convergence... -...done. Run time: 0.21 s +...done. Run time: 0.34 s *** Iteration 2 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre -out multiple_recombinations.iteration_2.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.27 s +...done. Run time: 0.43 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.32 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.51 s Reinserting gaps into the alignment... -...done. Run time: 0.32 s +...done. Run time: 0.51 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.34 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.55 s Checking for convergence... -...done. Run time: 0.34 s +...done. Run time: 0.55 s *** Iteration 3 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre -out multiple_recombinations.iteration_3.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.43 s +...done. Run time: 0.69 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.48 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.75 s Reinserting gaps into the alignment... -...done. Run time: 0.48 s +...done. Run time: 0.76 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.49 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.79 s Checking for convergence... -...done. Run time: 0.50 s +...done. Run time: 0.80 s *** Iteration 4 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre -out multiple_recombinations.iteration_4.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.61 s +...done. Run time: 0.96 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.65 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.03 s Reinserting gaps into the alignment... -...done. Run time: 0.65 s +...done. Run time: 1.03 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.67 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.06 s Checking for convergence... -...done. Run time: 0.67 s +...done. Run time: 1.07 s *** Iteration 5 *** Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -intree /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre -out multiple_recombinations.iteration_5.tre /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.77 s +...done. Run time: 1.21 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.81 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.28 s Reinserting gaps into the alignment... -...done. Run time: 0.81 s +...done. Run time: 1.28 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpxewa4shi/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.83 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpy16a5efb/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.32 s Checking for convergence... Convergence after 5 iterations: Tree observed before. @@ -1780,7 +1798,7 @@ Exiting the main loop. Creating the final output... -...finished. Total run time: 0.84 s +...finished. Total run time: 1.33 s --- Gubbins 2.4.1 --- @@ -1790,14 +1808,14 @@ ...done. Run time: 0.00 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Filtering input alignment... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.aln -...done. Run time: 0.02 s +gubbins /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.aln +...done. Run time: 0.03 s Entering the main loop. @@ -1805,108 +1823,108 @@ Constructing the phylogenetic tree with FastTree... FastTree -nosupport -gtr -gamma -nt -out multiple_recombinations.iteration_1.tre /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln > /dev/null 2>&1 -...done. Run time: 0.15 s +...done. Run time: 0.23 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.19 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.snp_sites.aln -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.31 s Reinserting gaps into the alignment... -...done. Run time: 0.20 s +...done. Run time: 0.31 s Running Gubbins to detect recombinations... -ok -test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies.test_iqtree) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.21 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.34 s Checking for convergence... -...done. Run time: 0.21 s +...done. Run time: 0.34 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.29 s +...done. Run time: 0.46 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.34 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.56 s Reinserting gaps into the alignment... -...done. Run time: 0.34 s +...done. Run time: 0.56 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.36 s +ok +test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies.test_iqtree) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.60 s Checking for convergence... -...done. Run time: 0.36 s +...done. Run time: 0.60 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.43 s +...done. Run time: 0.72 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.48 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.79 s Reinserting gaps into the alignment... -...done. Run time: 0.48 s +...done. Run time: 0.80 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.49 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.83 s Checking for convergence... -...done. Run time: 0.50 s +...done. Run time: 0.84 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 0.57 s +...done. Run time: 0.95 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.61 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.02 s Reinserting gaps into the alignment... -...done. Run time: 0.61 s +...done. Run time: 1.02 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.63 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.06 s Checking for convergence... -...done. Run time: 0.63 s +...done. Run time: 1.07 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 0.70 s +...done. Run time: 1.18 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.75 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.25 s Reinserting gaps into the alignment... -...done. Run time: 0.75 s +...done. Run time: 1.26 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpjs4nurru/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.77 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpn8dka62s/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.29 s Checking for convergence... -...done. Run time: 0.77 s +...done. Run time: 1.30 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 0.77 s +...finished. Total run time: 1.31 s --- Gubbins 2.4.1 --- @@ -1922,8 +1940,8 @@ ...done. Run time: 0.00 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.aln -...done. Run time: 0.01 s +gubbins /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.aln +...done. Run time: 0.02 s Entering the main loop. @@ -1931,108 +1949,109 @@ Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1 -nt 1 -quiet -...done. Run time: 0.66 s +...done. Run time: 1.36 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.iteration_1.tre.rooted -quiet -...done. Run time: 0.71 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_1.internal -nt 1 -te /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.iteration_1.tre.rooted -quiet +...done. Run time: 1.46 s Reinserting gaps into the alignment... -...done. Run time: 0.71 s +...done. Run time: 1.46 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.73 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.50 s Checking for convergence... -...done. Run time: 0.73 s +...done. Run time: 1.50 s *** Iteration 2 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -pre multiple_recombinations.iteration_2 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre -quiet -...done. Run time: 1.05 s +...done. Run time: 1.98 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_2.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.iteration_2.tre.rooted -quiet -...done. Run time: 1.08 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_2.internal -nt 1 -te /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.iteration_2.tre.rooted -quiet +...done. Run time: 2.05 s Reinserting gaps into the alignment... -...done. Run time: 1.09 s +...done. Run time: 2.06 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.10 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.09 s Checking for convergence... -...done. Run time: 1.10 s +...done. Run time: 2.09 s *** Iteration 3 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -pre multiple_recombinations.iteration_3 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre -quiet -...done. Run time: 1.31 s +...done. Run time: 2.26 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_3.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.iteration_3.tre.rooted -quiet -...done. Run time: 1.36 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_3.internal -nt 1 -te /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.iteration_3.tre.rooted -quiet +...done. Run time: 2.39 s Reinserting gaps into the alignment... -...done. Run time: 1.36 s +...done. Run time: 2.40 s Running Gubbins to detect recombinations... -ok -test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies.test_raxml) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.38 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.43 s Checking for convergence... -...done. Run time: 1.38 s +...done. Run time: 2.44 s *** Iteration 4 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -pre multiple_recombinations.iteration_4 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre -quiet -...done. Run time: 1.69 s +...done. Run time: 2.74 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_4.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.iteration_4.tre.rooted -quiet -...done. Run time: 1.74 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_4.internal -nt 1 -te /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.iteration_4.tre.rooted -quiet +...done. Run time: 2.82 s Reinserting gaps into the alignment... -...done. Run time: 1.74 s +...done. Run time: 2.83 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.76 s +ok +test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies.test_raxml) ... ok +test_rename_final_output (gubbins.tests.test_dependencies.TestExternalDependencies.test_rename_final_output) ... gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 2.86 s Checking for convergence... -...done. Run time: 1.76 s +...done. Run time: 2.87 s *** Iteration 5 *** Constructing the phylogenetic tree with iqtree2... iqtree2 -safe -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -pre multiple_recombinations.iteration_5 -nt 1 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre -quiet -...done. Run time: 2.30 s +...done. Run time: 3.08 s Reconstructing ancestral sequences with iqtree2... -iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_5.internal -nt 1 -te /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.iteration_5.tre.rooted -quiet -...done. Run time: 2.34 s +iqtree2 -safe -asr -m GTR+G4 -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -pre multiple_recombinations.iteration_5.internal -nt 1 -te /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.iteration_5.tre.rooted -quiet +...done. Run time: 3.16 s Reinserting gaps into the alignment... -...done. Run time: 2.35 s +...done. Run time: 3.16 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpi7ulregf/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 2.36 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmphrprmhc9/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 3.19 s Checking for convergence... -...done. Run time: 2.37 s +...done. Run time: 3.21 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 2.37 s +...finished. Total run time: 3.21 s --- Gubbins 2.4.1 --- @@ -2042,14 +2061,14 @@ ...done. Run time: 0.00 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Filtering input alignment... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.aln -...done. Run time: 0.01 s +gubbins /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.aln +...done. Run time: 0.03 s Entering the main loop. @@ -2057,114 +2076,107 @@ Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 -...done. Run time: 0.13 s +...done. Run time: 0.21 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.18 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.29 s Reinserting gaps into the alignment... -...done. Run time: 0.18 s +...done. Run time: 0.30 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.20 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.33 s Checking for convergence... -...done. Run time: 0.20 s +...done. Run time: 0.33 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.27 s +...done. Run time: 0.44 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.32 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.52 s Reinserting gaps into the alignment... -...done. Run time: 0.32 s +...done. Run time: 0.52 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.33 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.56 s Checking for convergence... -...done. Run time: 0.33 s +...done. Run time: 0.56 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.50 s +...done. Run time: 0.82 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.63 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.02 s Reinserting gaps into the alignment... -...done. Run time: 0.64 s +...done. Run time: 1.03 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.65 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.05 s Checking for convergence... -...done. Run time: 0.65 s +...done. Run time: 1.06 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 0.88 s +...done. Run time: 1.42 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.93 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.49 s Reinserting gaps into the alignment... -...done. Run time: 0.93 s +...done. Run time: 1.50 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.95 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.53 s Checking for convergence... -...done. Run time: 0.95 s +...done. Run time: 1.54 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 1.04 s +...done. Run time: 1.69 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.09 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.77 s Reinserting gaps into the alignment... -...done. Run time: 1.09 s +...done. Run time: 1.77 s Running Gubbins to detect recombinations... -ok -test_rename_final_output (gubbins.tests.test_dependencies.TestExternalDependencies.test_rename_final_output) ... ok - ----------------------------------------------------------------------- -Ran 67 tests in 7.435s - -OK -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp2s14p1i1/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.11 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp398bzf3t/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.81 s Checking for convergence... -...done. Run time: 1.12 s +...done. Run time: 1.82 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 1.12 s +...finished. Total run time: 1.83 s --- Gubbins 2.4.1 --- @@ -2174,14 +2186,14 @@ ...done. Run time: 0.00 s Checking input files... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Filtering input alignment... -...done. Run time: 0.00 s +...done. Run time: 0.01 s Running Gubbins to detect SNPs... -gubbins /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.aln -...done. Run time: 0.01 s +gubbins /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.aln +...done. Run time: 0.03 s Entering the main loop. @@ -2189,107 +2201,138 @@ Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1 > /dev/null 2>&1 -...done. Run time: 0.13 s +...done. Run time: 0.21 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.18 s +ok +test_are_all_sequence_names_unique (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_all_sequence_names_unique) ... ok +test_are_all_sequences_the_same_length (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_all_sequences_the_same_length) ... ok +test_are_there_enough_sequences_to_build_a_tree (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_are_there_enough_sequences_to_build_a_tree) ... ok +test_does_each_sequence_have_a_name (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_does_each_sequence_have_a_name) ... ok +test_does_the_sequence_have_sensible_characters (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_does_the_sequence_have_sensible_characters) ... ok +test_valid_fasta_file (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile.test_valid_fasta_file) ... ok +test_are_all_names_unique (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_are_all_names_unique) ... ok +test_do_the_names_match_the_fasta_file (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_do_the_names_match_the_fasta_file) ... ok +test_is_it_a_valid_newick_tree (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree.test_is_it_a_valid_newick_tree) ... ok + +---------------------------------------------------------------------- +Ran 67 tests in 11.470s + +OK +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_1.internal -t /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.iteration_1.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.29 s Reinserting gaps into the alignment... -...done. Run time: 0.18 s +...done. Run time: 0.30 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.20 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.aln -t multiple_recombinations.iteration_1.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.33 s Checking for convergence... -...done. Run time: 0.20 s +...done. Run time: 0.34 s *** Iteration 2 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre.phylip -n multiple_recombinations.iteration_2 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_1.tre > /dev/null 2>&1 -...done. Run time: 0.27 s +...done. Run time: 0.44 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.32 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_2.internal -t /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.iteration_2.tre.rooted > /dev/null 2>&1 +...done. Run time: 0.52 s Reinserting gaps into the alignment... -...done. Run time: 0.32 s +...done. Run time: 0.53 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.34 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.aln -t multiple_recombinations.iteration_2.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 0.56 s Checking for convergence... -...done. Run time: 0.34 s +...done. Run time: 0.56 s *** Iteration 3 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre.phylip -n multiple_recombinations.iteration_3 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_2.tre > /dev/null 2>&1 -...done. Run time: 0.51 s +...done. Run time: 0.82 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.64 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_3.internal -t /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.iteration_3.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.03 s Reinserting gaps into the alignment... -...done. Run time: 0.65 s +...done. Run time: 1.03 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.66 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.aln -t multiple_recombinations.iteration_3.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.06 s Checking for convergence... -...done. Run time: 0.66 s +...done. Run time: 1.07 s *** Iteration 4 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre.phylip -n multiple_recombinations.iteration_4 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_3.tre > /dev/null 2>&1 -...done. Run time: 0.89 s +...done. Run time: 1.42 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 -...done. Run time: 0.94 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_4.internal -t /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.iteration_4.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.50 s Reinserting gaps into the alignment... -...done. Run time: 0.94 s +...done. Run time: 1.51 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 0.96 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.aln -t multiple_recombinations.iteration_4.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.54 s Checking for convergence... -...done. Run time: 0.96 s +...done. Run time: 1.55 s *** Iteration 5 *** Constructing the phylogenetic tree with raxmlHPC... raxmlHPC -f d -p 1 -m GTRCAT -V -s /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre.phylip -n multiple_recombinations.iteration_5 -t /build/gubbins-2.4.1/python/multiple_recombinations.iteration_4.tre > /dev/null 2>&1 -...done. Run time: 1.06 s +...done. Run time: 1.70 s Reconstructing ancestral sequences with raxmlHPC... -raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 -...done. Run time: 1.11 s +raxmlHPC -f A -p 1 -m GTRGAMMA -s /build/gubbins-2.4.1/python/multiple_recombinations.aln.phylip -n multiple_recombinations.iteration_5.internal -t /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.iteration_5.tre.rooted > /dev/null 2>&1 +...done. Run time: 1.79 s Reinserting gaps into the alignment... -...done. Run time: 1.11 s +...done. Run time: 1.79 s Running Gubbins to detect recombinations... -gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmpsmz1xhgu/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln -...done. Run time: 1.13 s +gubbins -r -v multiple_recombinations.aln.gaps.vcf -a 100 -b 10000 -f /build/gubbins-2.4.1/python/tmp_uu52ffy/multiple_recombinations.aln -t multiple_recombinations.iteration_5.tre -m 3 multiple_recombinations.aln.gaps.snp_sites.aln +...done. Run time: 1.83 s Checking for convergence... -...done. Run time: 1.13 s +...done. Run time: 1.84 s Maximum number of iterations (5) reached. Exiting the main loop. Creating the final output... -...finished. Total run time: 1.13 s +...finished. Total run time: 1.84 s +All sequence names in the fasta file must be unique +Unexpected error: +Error with the input FASTA file: It is in the wrong format so check its an alignment +Unexpected error: +Error with the input FASTA file: It is in the wrong format so check its an alignment +Each sequence must be the same length +Error with input FASTA file: you need more than 3 sequences to build a meaningful tree +Each sequence must have a name and some genomic data +Error with the input FASTA file: One of the sequence names is blank +Error with the input FASTA file: One of the sequence names is blank +Each sequence must have a name and some genomic data +Error with the input FASTA file: One of the sequences contains odd characters, only ACGTNacgtn- are permitted +Error with the input FASTA file: One of the sequences contains odd characters, only ACGTNacgtn- are permitted +Each sequence must have a name and some genomic data +Error with the input starting tree: Is it a valid Newick file? +Error with the input starting tree: Is it a valid Newick file? make[1]: Leaving directory '/build/gubbins-2.4.1' create-stamp debian/debhelper-build-stamp dh_prep @@ -2301,8 +2344,8 @@ Making install in src make[3]: Entering directory '/build/gubbins-2.4.1/src' make[4]: Entering directory '/build/gubbins-2.4.1/src' - /bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu' + /usr/bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) @@ -2311,8 +2354,8 @@ libtool: install: chmod 644 /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: install: ranlib /build/gubbins-2.4.1/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' - /bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/gubbins-2.4.1/debian/gubbins/usr/bin' + /usr/bin/mkdir -p '/build/gubbins-2.4.1/debian/gubbins/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c gubbins '/build/gubbins-2.4.1/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/gubbins-2.4.1/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. @@ -2342,72 +2385,72 @@ running build_py creating build creating build/lib -creating build/lib/scripts -copying scripts/gubbins_drawer.py -> build/lib/scripts -copying scripts/__init__.py -> build/lib/scripts -copying scripts/run_gubbins.py -> build/lib/scripts creating build/lib/gubbins -copying gubbins/treebuilders.py -> build/lib/gubbins -copying gubbins/utils.py -> build/lib/gubbins -copying gubbins/PreProcessFasta.py -> build/lib/gubbins -copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins +copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins +copying gubbins/__init__.py -> build/lib/gubbins +copying gubbins/utils.py -> build/lib/gubbins +copying gubbins/treebuilders.py -> build/lib/gubbins +creating build/lib/scripts +copying scripts/run_gubbins.py -> build/lib/scripts +copying scripts/__init__.py -> build/lib/scripts +copying scripts/gubbins_drawer.py -> build/lib/scripts creating build/lib/gubbins/tests -copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests -copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests -copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests -copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests +copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests +copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests -copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests -copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests +copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests +copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests +copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests +copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests running install_lib creating ../debian/gubbins/usr/share creating ../debian/gubbins/usr/share/gubbins -creating ../debian/gubbins/usr/share/gubbins/scripts -copying build/lib/scripts/gubbins_drawer.py -> ../debian/gubbins/usr/share/gubbins/scripts -copying build/lib/scripts/__init__.py -> ../debian/gubbins/usr/share/gubbins/scripts -copying build/lib/scripts/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/scripts creating ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests -copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests +copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins -copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins -byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/gubbins_drawer.py to gubbins_drawer.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/__init__.py to __init__.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/run_gubbins.py to run_gubbins.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-311.pyc +copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins +copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins +creating ../debian/gubbins/usr/share/gubbins/scripts +copying build/lib/scripts/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/scripts +copying build/lib/scripts/__init__.py -> ../debian/gubbins/usr/share/gubbins/scripts +copying build/lib/scripts/gubbins_drawer.py -> ../debian/gubbins/usr/share/gubbins/scripts +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-311.pyc -byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-311.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/run_gubbins.py to run_gubbins.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/__init__.py to __init__.cpython-311.pyc +byte-compiling ../debian/gubbins/usr/share/gubbins/scripts/gubbins_drawer.py to gubbins_drawer.cpython-311.pyc running install_egg_info running egg_info writing gubbins.egg-info/PKG-INFO @@ -2447,9 +2490,9 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol @@ -2464,12 +2507,14 @@ 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/19165/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/19165/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/23082 and its subdirectories -I: Current time: Thu Jun 6 11:12:31 -12 2024 -I: pbuilder-time-stamp: 1717715551 +I: removing directory /srv/workspace/pbuilder/19165 and its subdirectories +I: Current time: Sat May 6 06:56:12 +14 2023 +I: pbuilder-time-stamp: 1683305772