1s autopkgtest [16:52:14]: starting date and time: 2025-03-15 16:52:14+0000 1s autopkgtest [16:52:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [16:52:14]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d0rlqm79/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade progressivemauve --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-25.secgroup --name adt-plucky-s390x-progressivemauve-20250315-165213-juju-7f2275-prod-proposed-migration-environment-15-e2ae8356-c8d6-4cc6-a74b-9c7c6ee4cff6 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 159s autopkgtest [16:54:52]: testbed dpkg architecture: s390x 159s autopkgtest [16:54:52]: testbed apt version: 2.9.33 160s autopkgtest [16:54:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 160s autopkgtest [16:54:53]: testbed release detected to be: None 161s autopkgtest [16:54:54]: updating testbed package index (apt update) 161s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 161s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 161s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 162s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 162s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 162s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 162s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 162s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 162s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 162s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 162s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 163s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 163s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 163s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 163s Fetched 1073 kB in 2s (585 kB/s) 163s Reading package lists... 164s + lsb_release --codename --short 164s Reading package lists...+ RELEASE=plucky 164s + cat 164s + [ plucky != trusty ] 164s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 164s 164s Building dependency tree... 164s Reading state information... 164s Calculating upgrade... 164s Calculating upgrade... 164s The following packages were automatically installed and are no longer required: 164s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 164s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 164s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 164s linux-tools-6.11.0-8-generic 164s Use 'sudo apt autoremove' to remove them. 164s The following packages will be upgraded: 164s pinentry-curses python3-jinja2 strace 165s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 652 kB of archives. 165s After this operation, 27.6 kB of additional disk space will be used. 165s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 165s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 165s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 166s Fetched 652 kB in 1s (642 kB/s) 166s (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 ... 81428 files and directories currently installed.) 166s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 166s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 166s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 166s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 166s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 166s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 166s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 166s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 166s Setting up strace (6.13+ds-1ubuntu1) ... 166s Processing triggers for man-db (2.13.0-1) ... 167s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 167s + /usr/lib/apt/apt-helper analyze-pattern ?true 167s + uname -r 167s + sed s/\./\\./g 167s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 167s + apt list ?obsolete 167s + tail -n+2 167s + cut -d/ -f1 167s + grep -v ^linux-.*6\.14\.0-10-generic.* 167s + obsolete_pkgs=linux-headers-6.11.0-8-generic 167s linux-headers-6.11.0-8 167s linux-modules-6.11.0-8-generic 167s linux-tools-6.11.0-8-generic 167s linux-tools-6.11.0-8 167s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s Solving dependencies... 167s The following packages will be REMOVED: 167s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 167s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 167s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 167s linux-tools-6.11.0-8-generic* 167s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 167s After this operation, 167 MB disk space will be freed. 167s (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 ... 81428 files and directories currently installed.) 167s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 167s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 167s Removing libpython3.12t64:s390x (3.12.9-1) ... 167s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 167s Removing libnsl2:s390x (1.3.0-3build3) ... 167s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 167s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 167s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 168s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 168s Processing triggers for libc-bin (2.41-1ubuntu1) ... 168s (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 ... 56328 files and directories currently installed.) 168s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 168s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 168s + grep -q trusty /etc/lsb-release 168s + [ ! -d /usr/share/doc/unattended-upgrades ] 168s + [ ! -d /usr/share/doc/lxd ] 168s + [ ! -d /usr/share/doc/lxd-client ] 168s + [ ! -d /usr/share/doc/snapd ] 168s + type iptables 168s + cat 168s + chmod 755 /etc/rc.local 168s + . /etc/rc.local 168s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 168s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 168s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 168s + uname -m 168s + [ s390x = ppc64le ] 168s + [ -d /run/systemd/system ] 168s + systemd-detect-virt --quiet --vm 168s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 168s + cat 168s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 168s + echo COMPRESS=lz4 168s autopkgtest [16:55:01]: upgrading testbed (apt dist-upgrade and autopurge) 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 169s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 169s Starting 2 pkgProblemResolver with broken count: 0 169s Done 169s Entering ResolveByKeep 169s 169s Calculating upgrade... 169s The following packages will be upgraded: 169s libc-bin libc-dev-bin libc6 libc6-dev locales 170s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 170s Need to get 9512 kB of archives. 170s After this operation, 8192 B of additional disk space will be used. 170s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 173s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 173s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 179s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 181s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 189s Preconfiguring packages ... 189s Fetched 9512 kB in 20s (482 kB/s) 189s (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 ... 56326 files and directories currently installed.) 189s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 189s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 189s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 189s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 189s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 190s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 190s Setting up libc6:s390x (2.41-1ubuntu2) ... 190s (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 ... 56326 files and directories currently installed.) 190s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 190s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 190s Setting up libc-bin (2.41-1ubuntu2) ... 190s (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 ... 56326 files and directories currently installed.) 190s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 190s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 190s Setting up locales (2.41-1ubuntu2) ... 190s Generating locales (this might take a while)... 191s en_US.UTF-8... done 191s Generation complete. 191s Setting up libc-dev-bin (2.41-1ubuntu2) ... 191s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 191s Processing triggers for man-db (2.13.0-1) ... 192s Processing triggers for systemd (257.3-1ubuntu3) ... 192s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s Starting pkgProblemResolver with broken count: 0 193s Starting 2 pkgProblemResolver with broken count: 0 193s Done 193s Solving dependencies... 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 193s autopkgtest [16:55:26]: rebooting testbed after setup commands that affected boot 215s autopkgtest [16:55:48]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 221s autopkgtest [16:55:54]: @@@@@@@@@@@@@@@@@@@@ apt-source progressivemauve 223s Get:1 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (dsc) [2413 B] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (tar) [96.1 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/universe progressivemauve 1.2.0+4713+dfsg-5build3 (diff) [18.1 kB] 223s gpgv: Signature made Mon Apr 8 15:02:20 2024 UTC 223s gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 223s gpgv: issuer "juliank@ubuntu.com" 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./progressivemauve_1.2.0+4713+dfsg-5build3.dsc: no acceptable signature found 223s autopkgtest [16:55:56]: testing package progressivemauve version 1.2.0+4713+dfsg-5build3 224s autopkgtest [16:55:57]: build not needed 224s autopkgtest [16:55:57]: test run-unit-test: preparing testbed 224s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 225s The following NEW packages will be installed: 225s libboost-filesystem1.83.0 libboost-iostreams1.83.0 225s libboost-program-options1.83.0 libgenome0 libgomp1 libmems1t64 libmuscle1 225s progressivemauve 225s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 225s Need to get 2884 kB of archives. 225s After this operation, 14.8 MB of additional disk space will be used. 225s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-filesystem1.83.0 s390x 1.83.0-4.1ubuntu2 [288 kB] 226s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-iostreams1.83.0 s390x 1.83.0-4.1ubuntu2 [259 kB] 226s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libboost-program-options1.83.0 s390x 1.83.0-4.1ubuntu2 [326 kB] 226s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libgenome0 s390x 1.3.11+svn20110227.4616-6 [120 kB] 227s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 227s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libmuscle1 s390x 3.7+4565-8 [259 kB] 227s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libmems1t64 s390x 1.6.0+4725-11 [586 kB] 228s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x progressivemauve s390x 1.2.0+4713+dfsg-5build3 [894 kB] 230s Fetched 2884 kB in 5s (571 kB/s) 230s Selecting previously unselected package libboost-filesystem1.83.0:s390x. 230s (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 ... 56326 files and directories currently installed.) 230s Preparing to unpack .../0-libboost-filesystem1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 230s Unpacking libboost-filesystem1.83.0:s390x (1.83.0-4.1ubuntu2) ... 230s Selecting previously unselected package libboost-iostreams1.83.0:s390x. 230s Preparing to unpack .../1-libboost-iostreams1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 230s Unpacking libboost-iostreams1.83.0:s390x (1.83.0-4.1ubuntu2) ... 230s Selecting previously unselected package libboost-program-options1.83.0:s390x. 230s Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-4.1ubuntu2_s390x.deb ... 230s Unpacking libboost-program-options1.83.0:s390x (1.83.0-4.1ubuntu2) ... 230s Selecting previously unselected package libgenome0:s390x. 230s Preparing to unpack .../3-libgenome0_1.3.11+svn20110227.4616-6_s390x.deb ... 230s Unpacking libgenome0:s390x (1.3.11+svn20110227.4616-6) ... 230s Selecting previously unselected package libgomp1:s390x. 230s Preparing to unpack .../4-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 230s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 230s Selecting previously unselected package libmuscle1. 230s Preparing to unpack .../5-libmuscle1_3.7+4565-8_s390x.deb ... 230s Unpacking libmuscle1 (3.7+4565-8) ... 230s Selecting previously unselected package libmems1t64:s390x. 230s Preparing to unpack .../6-libmems1t64_1.6.0+4725-11_s390x.deb ... 230s Unpacking libmems1t64:s390x (1.6.0+4725-11) ... 230s Selecting previously unselected package progressivemauve. 230s Preparing to unpack .../7-progressivemauve_1.2.0+4713+dfsg-5build3_s390x.deb ... 230s Unpacking progressivemauve (1.2.0+4713+dfsg-5build3) ... 230s Setting up libboost-program-options1.83.0:s390x (1.83.0-4.1ubuntu2) ... 230s Setting up libgenome0:s390x (1.3.11+svn20110227.4616-6) ... 230s Setting up libboost-filesystem1.83.0:s390x (1.83.0-4.1ubuntu2) ... 230s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 230s Setting up libboost-iostreams1.83.0:s390x (1.83.0-4.1ubuntu2) ... 230s Setting up libmuscle1 (3.7+4565-8) ... 230s Setting up libmems1t64:s390x (1.6.0+4725-11) ... 230s Setting up progressivemauve (1.2.0+4713+dfsg-5build3) ... 230s Processing triggers for man-db (2.13.0-1) ... 231s Processing triggers for libc-bin (2.41-1ubuntu2) ... 232s autopkgtest [16:56:05]: test run-unit-test: [----------------------- 232s Storing raw sequence at /tmp/rawseq1426.000 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Storing raw sequence at /tmp/rawseq1426.001 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Storing raw sequence at /tmp/rawseq1426.002 232s Sequence loaded successfully. 232s genome_3.gbk 2224 base pairs. 232s Using weight 9 mers for initial seeds 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s 33%.. 232s 66%.. 232s 99%.. 232s done. 232s using default bp penalty: 77720 232s using default bp estimate min score: 233160 232s Starting with 152 multi-matches 232s Computing genome content distance matrix... 232s 232s 232s Genome conservation distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s Writing guide tree to /tmp/guide_tree1426.000 232s reading tree... 232s initializing alignment tree... 232s Constructing seed occurrence lists for repeat detection 232s Calculating pairwise breakpoint distances 232s Pair 0, 1 has 30 initial LCBs 232s Using scaled bp penalty: 22995.7 232s Pair (0,1) has 1 well-supported breakpoints 232s Pair 0, 2 has 29 initial LCBs 232s Using scaled bp penalty: 10025.6 232s Pair (0,2) has 1 well-supported breakpoints 232s Pair 1, 2 has 31 initial LCBs 232s Using scaled bp penalty: 13766.1 232s Pair (1,2) has 1 well-supported breakpoints 232s genome content distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s bp distance matrix: 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 232s Aligning... 232s Aligning node 2 to 3 via 1! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 44 tracking matches 232s There are 88 / 220 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 27 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 3%..7%.. 232s 11%..14%..18%.. 232s 22%..25%..29%.. 232s 33%..37%.. 232s 40%..44%..48%.. 232s 51%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 57862 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 0,0 has an additional 5 matches 232s Restoring backed up alignment tree... 232s 1,0 has 5 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 35 tracking matches 232s There are 70 / 175 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 7 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 232s 14%.. 232s 28%..done 232s Arrived at 3 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 8 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 3 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 57862, new anchor score: 50704 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Aligning node 1 to 4 via 0! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 60 tracking matches 232s There are 239 / 300 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 89 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 1%..2%..3%..4%..5%..6%..7%..8%.. 232s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 232s 20%..21%..22%..23%..24%..25%..26%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 5 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 99201 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 3 new matches outside LCBs 232s 1,0 have 1 new matches outside LCBs 232s 0,0 has an additional 3 matches 232s 1,0 has an additional 1 matches 232s Restoring backed up alignment tree... 232s 0,2 has 3 pairwise matches 232s 1,2 has 1 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 99201, new anchor score: 102789 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 1,0 have 0 new matches outside LCBs 232s Restoring backed up alignment tree... 232s 0,2 has 0 pairwise matches 232s 1,2 has 0 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 102789, new anchor score: 102789 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Performing final pass iterative refinement 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s root alignment has 1 superintervals 232s root alignment length: 2328 232s Organisms have 52.8% GC 232s Storing raw sequence at /tmp/rawseq1427.000 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Storing raw sequence at /tmp/rawseq1427.001 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Storing raw sequence at /tmp/rawseq1427.002 232s Sequence loaded successfully. 232s genome_3.gbk 2224 base pairs. 232s Using weight 9 mers for initial seeds 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s 33%.. 232s 66%.. 232s 99%.. 232s done. 232s using default bp penalty: 77720 232s using default bp estimate min score: 233160 232s Starting with 152 multi-matches 232s Computing genome content distance matrix... 232s 232s 232s Genome conservation distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s Writing guide tree to threeway.tree 232s reading tree... 232s initializing alignment tree... 232s Constructing seed occurrence lists for repeat detection 232s Calculating pairwise breakpoint distances 232s Pair 0, 1 has 30 initial LCBs 232s Using scaled bp penalty: 22995.7 232s Pair (0,1) has 1 well-supported breakpoints 232s Pair 0, 2 has 29 initial LCBs 232s Using scaled bp penalty: 10025.6 232s Pair (0,2) has 1 well-supported breakpoints 232s Pair 1, 2 has 31 initial LCBs 232s Using scaled bp penalty: 13766.1 232s Pair (1,2) has 1 well-supported breakpoints 232s genome content distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s bp distance matrix: 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 232s Aligning... 232s Aligning node 2 to 3 via 1! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 44 tracking matches 232s There are 88 / 220 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 27 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 3%..7%.. 232s 11%..14%..18%.. 232s 22%..25%..29%.. 232s 33%..37%.. 232s 40%..44%..48%.. 232s 51%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 57862 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 0,0 has an additional 5 matches 232s Restoring backed up alignment tree... 232s 1,0 has 5 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 35 tracking matches 232s There are 70 / 175 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 7 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 232s 14%.. 232s 28%..done 232s Arrived at 3 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 8 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 3 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 57862, new anchor score: 50704 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Aligning node 1 to 4 via 0! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 60 tracking matches 232s There are 239 / 300 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 89 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 1%..2%..3%..4%..5%..6%..7%..8%.. 232s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 232s 20%..21%..22%..23%..24%..25%..26%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 5 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 99201 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 3 new matches outside LCBs 232s 1,0 have 1 new matches outside LCBs 232s 0,0 has an additional 3 matches 232s 1,0 has an additional 1 matches 232s Restoring backed up alignment tree... 232s 0,2 has 3 pairwise matches 232s 1,2 has 1 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 99201, new anchor score: 102789 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 1,0 have 0 new matches outside LCBs 232s Restoring backed up alignment tree... 232s 0,2 has 0 pairwise matches 232s 1,2 has 0 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 102789, new anchor score: 102789 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Performing final pass iterative refinement 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s root alignment has 1 superintervals 232s root alignment length: 2328 232s Organisms have 52.8% GC 232s Storing raw sequence at /tmp/rawseq1428.000 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Storing raw sequence at /tmp/rawseq1428.001 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Storing raw sequence at /tmp/rawseq1428.002 232s Sequence loaded successfully. 232s genome_3.gbk 2224 base pairs. 232s Using weight 9 mers for initial seeds 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s 33%.. 232s 66%.. 232s 99%.. 232s done. 232s using default bp penalty: 77720 232s using default bp estimate min score: 233160 232s Starting with 152 multi-matches 232s Computing genome content distance matrix... 232s 232s 232s Genome conservation distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s Writing guide tree to /tmp/guide_tree1428.000 232s reading tree... 232s initializing alignment tree... 232s Constructing seed occurrence lists for repeat detection 232s Calculating pairwise breakpoint distances 232s Pair 0, 1 has 30 initial LCBs 232s Using scaled bp penalty: 22995.7 232s Pair (0,1) has 1 well-supported breakpoints 232s Pair 0, 2 has 29 initial LCBs 232s Using scaled bp penalty: 10025.6 232s Pair (0,2) has 1 well-supported breakpoints 232s Pair 1, 2 has 31 initial LCBs 232s Using scaled bp penalty: 13766.1 232s Pair (1,2) has 1 well-supported breakpoints 232s genome content distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s bp distance matrix: 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 232s Aligning... 232s Aligning node 2 to 3 via 1! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 44 tracking matches 232s There are 88 / 220 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 27 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 3%..7%.. 232s 11%..14%..18%.. 232s 22%..25%..29%.. 232s 33%..37%.. 232s 40%..44%..48%.. 232s 51%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 57862 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 0,0 has an additional 5 matches 232s Restoring backed up alignment tree... 232s 1,0 has 5 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 35 tracking matches 232s There are 70 / 175 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 7 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 232s 14%.. 232s 28%..done 232s Arrived at 3 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 8 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 3 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 57862, new anchor score: 50704 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Aligning node 1 to 4 via 0! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 60 tracking matches 232s There are 239 / 300 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 89 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 1%..2%..3%..4%..5%..6%..7%..8%.. 232s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 232s 20%..21%..22%..23%..24%..25%..26%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 5 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 99201 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 3 new matches outside LCBs 232s 1,0 have 1 new matches outside LCBs 232s 0,0 has an additional 3 matches 232s 1,0 has an additional 1 matches 232s Restoring backed up alignment tree... 232s 0,2 has 3 pairwise matches 232s 1,2 has 1 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 99201, new anchor score: 102789 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 1,0 have 0 new matches outside LCBs 232s Restoring backed up alignment tree... 232s 0,2 has 0 pairwise matches 232s 1,2 has 0 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 102789, new anchor score: 102789 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Performing final pass iterative refinement 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s root alignment has 1 superintervals 232s root alignment length: 2328 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Sequence loaded successfully. 232s genome_3.gbk 2224 base pairs. 232s Organisms have 52.8% GC 232s Storing raw sequence at /tmp/rawseq1430.000 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Storing raw sequence at /tmp/rawseq1430.001 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Storing raw sequence at /tmp/rawseq1430.002 232s Sequence loaded successfully. 232s genome_3.gbk 2224 base pairs. 232s Using weight 9 mers for initial seeds 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s 33%.. 232s 66%.. 232s 99%.. 232s done. 232s Storing raw sequence at /tmp/rawseq1431.000 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Storing raw sequence at /tmp/rawseq1431.001 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Storing raw sequence at /tmp/rawseq1431.002 232s Sequence loaded successfully. 232s genome_3.gbk 2224 base pairs. 232s Using weight 9 mers for initial seeds 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s using default bp penalty: 77720 232s using default bp estimate min score: 233160 232s Starting with 152 multi-matches 232s Computing genome content distance matrix... 232s 232s 232s Genome conservation distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s Writing guide tree to /tmp/guide_tree1431.000 232s reading tree... 232s initializing alignment tree... 232s Constructing seed occurrence lists for repeat detection 232s Calculating pairwise breakpoint distances 232s Pair 0, 1 has 30 initial LCBs 232s Using scaled bp penalty: 22995.7 232s Pair (0,1) has 1 well-supported breakpoints 232s Pair 0, 2 has 29 initial LCBs 232s Using scaled bp penalty: 10025.6 232s Pair (0,2) has 1 well-supported breakpoints 232s Pair 1, 2 has 31 initial LCBs 232s Using scaled bp penalty: 13766.1 232s Pair (1,2) has 1 well-supported breakpoints 232s genome content distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s bp distance matrix: 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 232s Aligning... 232s Aligning node 2 to 3 via 1! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 44 tracking matches 232s There are 88 / 220 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 27 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 3%..7%.. 232s 11%..14%..18%.. 232s 22%..25%..29%.. 232s 33%..37%.. 232s 40%..44%..48%.. 232s 51%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 57862 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 0,0 has an additional 5 matches 232s Restoring backed up alignment tree... 232s 1,0 has 5 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 35 tracking matches 232s There are 70 / 175 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 7 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 232s 14%.. 232s 28%..done 232s Arrived at 3 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 8 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 3 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 57862, new anchor score: 50704 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Aligning node 1 to 4 via 0! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 60 tracking matches 232s There are 239 / 300 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 89 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 1%..2%..3%..4%..5%..6%..7%..8%.. 232s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 232s 20%..21%..22%..23%..24%..25%..26%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 5 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 99201 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 3 new matches outside LCBs 232s 1,0 have 1 new matches outside LCBs 232s 0,0 has an additional 3 matches 232s 1,0 has an additional 1 matches 232s Restoring backed up alignment tree... 232s 0,2 has 3 pairwise matches 232s 1,2 has 1 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 99201, new anchor score: 102789 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 1,0 have 0 new matches outside LCBs 232s Restoring backed up alignment tree... 232s 0,2 has 0 pairwise matches 232s 1,2 has 0 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 102789, new anchor score: 102789 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Performing final pass iterative refinement 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s root alignment has 1 superintervals 232s root alignment length: 2328 232s Organisms have 52.8% GC 232s Storing raw sequence at /tmp/rawseq1432.000 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Storing raw sequence at /tmp/rawseq1432.001 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Using weight 9 mers for initial seeds 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s 49%.. 232s 99%.. 232s done. 232s using default bp penalty: 50000 232s using default bp estimate min score: 232989 232s Exception FileNotOpened thrown from 232s Unknown() in gnFileSource.cpp 67 232s Called by Unknown() 232s Starting with 55 multi-matches 232s Computing genome content distance matrix... 232s 232s 232s Genome conservation distance matrix: 232s 0 0.4396 232s 0.4396 0 232s 232s Writing guide tree to /tmp/guide_tree1432.000 232s reading tree... 232s initializing alignment tree... 232s Constructing seed occurrence lists for repeat detection 232s Calculating pairwise breakpoint distances 232s Pair 0, 1 has 30 initial LCBs 232s Using scaled bp penalty: 22978.9 232s Pair (0,1) has 1 well-supported breakpoints 232s genome content distance matrix: 232s 0 0.4396 232s 0.4396 0 232s 232s bp distance matrix: 232s 0.9 0.9 232s 0.9 0.9 232s 232s Aligning... 232s Aligning node 1 to 2 via 0! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 44 tracking matches 232s There are 88 / 132 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 27 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 3%..7%.. 232s 11%..14%..18%.. 232s 22%..25%..29%.. 232s 33%..37%.. 232s 40%..44%..48%.. 232s 51%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(2) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 57862 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 0,0 has an additional 5 matches 232s Restoring backed up alignment tree... 232s 1,0 has 5 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 35 tracking matches 232s There are 70 / 105 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 7 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 4000 232s 232s 14%.. 232s 28%..done 232s Arrived at 3 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 8 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(2) has 1 intervals 232s propagateDescendantBreakpoints yields 3 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 57862, new anchor score: 50704 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Performing final pass iterative refinement 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s root alignment has 1 superintervals 232s root alignment length: 2249 232s Organisms have 53.2% GC 232s Storing raw sequence at /tmp/rawseq1433.000 232s Sequence loaded successfully. 232s genome_1.gbk 2175 base pairs. 232s Storing raw sequence at /tmp/rawseq1433.001 232s Sequence loaded successfully. 232s genome_2.gbk 2199 base pairs. 232s Storing raw sequence at /tmp/rawseq1433.002 232s Sequence loaded successfully. 232s genome_3.gbk 2224 base pairs. 232s Using weight 9 mers for initial seeds 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s Sorted mer list loaded successfully 232s 33%.. 232s 66%.. 232s 99%.. 232s done. 232s using default bp penalty: 77720 232s using default bp estimate min score: 233160 232s Starting with 152 multi-matches 232s Computing genome content distance matrix... 232s 232s 232s Genome conservation distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s Writing guide tree to /tmp/guide_tree1433.000 232s reading tree... 232s initializing alignment tree... 232s Constructing seed occurrence lists for repeat detection 232s Calculating pairwise breakpoint distances 232s Pair 0, 1 has 30 initial LCBs 232s Using scaled bp penalty: 22995.7 232s Pair (0,1) has 1 well-supported breakpoints 232s Pair 0, 2 has 29 initial LCBs 232s Using scaled bp penalty: 10025.6 232s Pair (0,2) has 1 well-supported breakpoints 232s Pair 1, 2 has 31 initial LCBs 232s Using scaled bp penalty: 13766.1 232s Pair (1,2) has 1 well-supported breakpoints 232s genome content distance matrix: 232s 0 0.4396 0.54463 232s 0.4396 0 0.507065 232s 0.54463 0.507065 0 232s 232s bp distance matrix: 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 0.9 0.9 0.9 232s 232s Aligning... 232s Aligning node 2 to 3 via 1! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 44 tracking matches 232s There are 88 / 220 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 27 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 5000 232s 3%..7%.. 232s 11%..14%..18%.. 232s 22%..25%..29%.. 232s 33%..37%.. 232s 40%..44%..48%.. 232s 51%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 57862 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 0,0 has an additional 5 matches 232s Restoring backed up alignment tree... 232s 1,0 has 5 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 35 tracking matches 232s There are 70 / 175 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 7 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.4396 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 5000 232s 232s 14%.. 232s 28%..done 232s Arrived at 3 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 8 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(2) has 1 intervals 232s descendant 1(3) has 1 intervals 232s propagateDescendantBreakpoints yields 3 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 57862, new anchor score: 48704 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Aligning node 1 to 4 via 0! 232s get ancestral matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 60 tracking matches 232s There are 239 / 300 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 89 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 5000 232s 1%..2%..3%..4%..5%..6%..7%..8%.. 232s 10%..11%..12%..13%..14%..15%..16%..17%..19%.. 232s 20%..21%..22%..23%..24%..25%..26%..done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 5 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: -1.79769e+308, new anchor score: 99201 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 3 new matches outside LCBs 232s 1,0 have 1 new matches outside LCBs 232s 0,0 has an additional 3 matches 232s 1,0 has an additional 1 matches 232s Restoring backed up alignment tree... 232s 0,2 has 3 pairwise matches 232s 1,2 has 1 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 5000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 99201, new anchor score: 102789 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 1,0 have 0 new matches outside LCBs 232s Restoring backed up alignment tree... 232s 0,2 has 0 pairwise matches 232s 1,2 has 0 pairwise matches 232s Performing Sum-of-pairs Greedy Breakpoint Elimination 232s construct LCB tracking matches 232s There are 38 tracking matches 232s There are 152 / 190 components used 232s init tracking match LCB tracking 232s pairwise score tracking matches 232s get pairwise LCBs 232s there are 2 pairwise LCBs 232s scaling bp penalty by conservation weight: 232s 0.54463 232s 0.507065 232s 232s 232s scaling bp penalty by bp weight: 232s 0.9 232s 0.9 232s 232s Greedy BPE 232s Scoring with scaled breakpoint penalty: 5000 232s done 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Previous anchoring score: 102789, new anchor score: 102789 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Performing final pass iterative refinement 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s root alignment has 1 superintervals 232s root alignment length: 2328 232s Organisms have 52.8% GC 232s Sequence loaded successfully. 232s all_virii.fasta 2175 base pairs. 232s Sequence loaded successfully. 232s all_virii.fasta 2199 base pairs. 232s Sequence loaded successfully. 232s all_virii.fasta 2224 base pairs. 232s Using 9-mers for initial seeds 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s 232s Searching with seed pattern 11100100100100111 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s 32%.. 232s 65%.. 232s 99%.. 232s 232s Searching with seed pattern 111001010100111 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s 33%.. 232s 66%.. 232s 99%.. 232s 232s Searching with seed pattern 111010010010111 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s Creating sorted mer list 232s Create time was: 0 seconds. 232s 32%.. 232s 65%.. 232s 99%.. 232s done 232s using default bp penalty: 77720 232s using default bp estimate min score: 233160 232s 232s Assuming collinear genomes... 232s Starting with 291 multi-matches 232s Computing genome content distance matrix... 232s 232s 232s Genome conservation distance matrix: 232s 0 0.220697 0.310296 232s 0.220697 0 0.291861 232s 0.310296 0.291861 0 232s 232s Writing guide tree to /tmp/guide_tree1434.000 232s reading tree... 232s initializing alignment tree... 232s Aligning... 232s Aligning node 3 to 4 via 1! 232s get ancestral matches 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(3) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Prev alignment len: 18446744073709551615, new alignment length: 3832 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s Restoring backed up alignment tree... 232s 1,0 has 0 pairwise matches 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(3) has 1 intervals 232s descendant 1(4) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Prev alignment len: 3832, new alignment length: 3832 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Aligning node 1 to 2 via 0! 232s get ancestral matches 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 5 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(2) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Prev alignment len: 18446744073709551615, new alignment length: 4373 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 14 new matches outside LCBs 232s 1,0 have 17 new matches outside LCBs 232s 0,0 has an additional 38 matches 232s 1,0 has an additional 41 matches 232s Restoring backed up alignment tree... 232s 0,2 has 38 pairwise matches 232s 1,2 has 41 pairwise matches 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 3 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(2) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Prev alignment len: 4373, new alignment length: 3825 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 2 new matches outside LCBs 232s 1,0 have 1 new matches outside LCBs 232s 0,0 has an additional 2 matches 232s 1,0 has an additional 1 matches 232s Restoring backed up alignment tree... 232s 0,2 has 2 pairwise matches 232s 1,2 has 1 pairwise matches 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 1 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(2) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Prev alignment len: 3825, new alignment length: 3802 232s Backing up alignment tree... 232s propagating ancestral breakpoints 232s recursive anchor search 232s 0,0 have 0 new matches outside LCBs 232s 1,0 have 0 new matches outside LCBs 232s Restoring backed up alignment tree... 232s 0,2 has 0 pairwise matches 232s 1,2 has 0 pairwise matches 232s Arrived at 1 intervals 232s Adding unaligned intervals 232s addUnalignedIntervals yields 1 intervals 232s Merging unaligned intervals 232s Marbling gaps 232s Propagating descendant breakpoints 232s descendant 0(1) has 1 intervals 232s descendant 1(2) has 1 intervals 232s propagateDescendantBreakpoints yields 1 intervals 232s Creating ancestral ordering 232s Prev alignment len: 3802, new alignment length: 3802 232s propagating ancestral breakpoints 232s performing a gapped alignment 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s Performing final pass iterative refinement 232s 232s 0%.. 232s 100%..Fix left ends 232s 232s done. 232s root alignment has 1 superintervals 232s root alignment length: 2328 233s autopkgtest [16:56:06]: test run-unit-test: -----------------------] 233s run-unit-test PASS 233s autopkgtest [16:56:06]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 234s autopkgtest [16:56:07]: @@@@@@@@@@@@@@@@@@@@ summary 234s run-unit-test PASS 251s nova [W] Using flock in prodstack6-s390x 251s Creating nova instance adt-plucky-s390x-progressivemauve-20250315-165213-juju-7f2275-prod-proposed-migration-environment-15-e2ae8356-c8d6-4cc6-a74b-9c7c6ee4cff6 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 251s nova [W] Timed out waiting for 40bbff5d-49d6-485d-812d-00c67fb713c6 to get deleted.