0s autopkgtest [22:48:20]: starting date and time: 2025-02-15 22:48:20+0000 0s autopkgtest [22:48:20]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:48:20]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k87yvp8f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade stacks --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-1.secgroup --name adt-plucky-ppc64el-stacks-20250215-224820-juju-7f2275-prod-proposed-migration-environment-20-c5f3f1bf-165f-41be-b52b-3a952d541982 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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/ 113s autopkgtest [22:50:13]: testbed dpkg architecture: ppc64el 113s autopkgtest [22:50:13]: testbed apt version: 2.9.28 114s autopkgtest [22:50:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s autopkgtest [22:50:14]: testbed release detected to be: None 115s autopkgtest [22:50:15]: updating testbed package index (apt update) 115s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 115s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 115s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 115s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [828 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 116s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.3 kB] 116s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [165 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [760 B] 116s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [922 kB] 116s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [4228 B] 116s Fetched 2121 kB in 1s (1940 kB/s) 117s Reading package lists... 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s The following packages will be upgraded: 118s dash gcc-14-base libatomic1 libgcc-s1 libstdc++6 libtasn1-6 libxdmcp6 118s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 1171 kB of archives. 118s After this operation, 15.4 kB of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el dash ppc64el 0.5.12-12ubuntu1 [114 kB] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libatomic1 ppc64el 14.2.0-17ubuntu1 [10.7 kB] 118s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-base ppc64el 14.2.0-17ubuntu1 [53.6 kB] 118s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++6 ppc64el 14.2.0-17ubuntu1 [886 kB] 119s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-s1 ppc64el 14.2.0-17ubuntu1 [39.2 kB] 119s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtasn1-6 ppc64el 4.20.0-2 [55.9 kB] 119s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxdmcp6 ppc64el 1:1.1.5-1 [11.6 kB] 119s Preconfiguring packages ... 119s Fetched 1171 kB in 1s (1944 kB/s) 119s (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 ... 106311 files and directories currently installed.) 119s Preparing to unpack .../dash_0.5.12-12ubuntu1_ppc64el.deb ... 119s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 119s Setting up dash (0.5.12-12ubuntu1) ... 119s (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 ... 106311 files and directories currently installed.) 119s Preparing to unpack .../libatomic1_14.2.0-17ubuntu1_ppc64el.deb ... 119s Unpacking libatomic1:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 119s Preparing to unpack .../gcc-14-base_14.2.0-17ubuntu1_ppc64el.deb ... 119s Unpacking gcc-14-base:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 119s Setting up gcc-14-base:ppc64el (14.2.0-17ubuntu1) ... 119s (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 ... 106311 files and directories currently installed.) 119s Preparing to unpack .../libstdc++6_14.2.0-17ubuntu1_ppc64el.deb ... 119s Unpacking libstdc++6:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 119s Setting up libstdc++6:ppc64el (14.2.0-17ubuntu1) ... 120s (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 ... 106311 files and directories currently installed.) 120s Preparing to unpack .../libgcc-s1_14.2.0-17ubuntu1_ppc64el.deb ... 120s Unpacking libgcc-s1:ppc64el (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 120s Setting up libgcc-s1:ppc64el (14.2.0-17ubuntu1) ... 120s (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 ... 106311 files and directories currently installed.) 120s Preparing to unpack .../libtasn1-6_4.20.0-2_ppc64el.deb ... 120s Unpacking libtasn1-6:ppc64el (4.20.0-2) over (4.19.0-3build1) ... 120s Preparing to unpack .../libxdmcp6_1%3a1.1.5-1_ppc64el.deb ... 120s Unpacking libxdmcp6:ppc64el (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 120s Setting up libxdmcp6:ppc64el (1:1.1.5-1) ... 120s Setting up libatomic1:ppc64el (14.2.0-17ubuntu1) ... 120s Setting up libtasn1-6:ppc64el (4.20.0-2) ... 120s Processing triggers for libc-bin (2.40-4ubuntu1) ... 120s Processing triggers for man-db (2.13.0-1) ... 120s Processing triggers for debianutils (5.21) ... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 121s autopkgtest [22:50:21]: upgrading testbed (apt dist-upgrade and autopurge) 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 122s Starting 2 pkgProblemResolver with broken count: 0 122s Done 122s Entering ResolveByKeep 122s 123s The following packages will be upgraded: 123s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 123s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Need to get 11.7 MB of archives. 123s After this operation, 358 kB of additional disk space will be used. 123s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc-dev-bin ppc64el 2.41-1ubuntu1 [25.3 kB] 123s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc6-dev ppc64el 2.41-1ubuntu1 [2046 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el locales all 2.41-1ubuntu1 [4246 kB] 123s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc6 ppc64el 2.41-1ubuntu1 [3243 kB] 124s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libc-bin ppc64el 2.41-1ubuntu1 [742 kB] 124s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el iproute2 ppc64el 6.13.0-1ubuntu1 [1419 kB] 124s Preconfiguring packages ... 124s Fetched 11.7 MB in 1s (10.5 MB/s) 124s (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 ... 106311 files and directories currently installed.) 124s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_ppc64el.deb ... 124s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 124s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_ppc64el.deb ... 124s Unpacking libc6-dev:ppc64el (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 124s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 124s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 125s Preparing to unpack .../libc6_2.41-1ubuntu1_ppc64el.deb ... 125s Checking for services that may need to be restarted... 125s Checking init scripts... 125s Checking for services that may need to be restarted... 125s Checking init scripts... 125s Stopping some services possibly affected by the upgrade (will be restarted later): 125s cron: stopping...done. 125s 125s Unpacking libc6:ppc64el (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 125s Setting up libc6:ppc64el (2.41-1ubuntu1) ... 125s Checking for services that may need to be restarted... 125s Checking init scripts... 125s Restarting services possibly affected by the upgrade: 125s cron: restarting...done. 125s 125s Services restarted successfully. 125s (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 ... 106312 files and directories currently installed.) 125s Preparing to unpack .../libc-bin_2.41-1ubuntu1_ppc64el.deb ... 125s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 125s Setting up libc-bin (2.41-1ubuntu1) ... 126s (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 ... 106312 files and directories currently installed.) 126s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_ppc64el.deb ... 126s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 126s Setting up iproute2 (6.13.0-1ubuntu1) ... 126s Setting up locales (2.41-1ubuntu1) ... 126s Installing new version of config file /etc/locale.alias ... 127s Generating locales (this might take a while)... 128s en_US.UTF-8... done 128s Generation complete. 128s Setting up libc-dev-bin (2.41-1ubuntu1) ... 128s Setting up libc6-dev:ppc64el (2.41-1ubuntu1) ... 128s Processing triggers for man-db (2.13.0-1) ... 129s Processing triggers for systemd (257.2-3ubuntu1) ... 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 131s Starting pkgProblemResolver with broken count: 0 131s Starting 2 pkgProblemResolver with broken count: 0 131s Done 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s autopkgtest [22:50:33]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 16:32:08 UTC 2025 134s autopkgtest [22:50:34]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 135s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (dsc) [2070 B] 135s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (tar) [371 kB] 135s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (diff) [12.2 kB] 136s gpgv: Signature made Sat Aug 31 10:00:49 2024 UTC 136s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 136s gpgv: issuer "emollier@debian.org" 136s gpgv: Can't check signature: No public key 136s dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-1.dsc: no acceptable signature found 136s autopkgtest [22:50:36]: testing package stacks version 2.68+dfsg-1 136s autopkgtest [22:50:36]: build not needed 137s autopkgtest [22:50:37]: test run-unit-test: preparing testbed 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 137s The following NEW packages will be installed: 137s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 138s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 138s Need to get 3637 kB of archives. 138s After this operation, 11.9 MB of additional disk space will be used. 138s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdbi-perl ppc64el 1.647-1 [837 kB] 138s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.23-1 [63.4 kB] 138s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-17ubuntu1 [161 kB] 138s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB] 138s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.21+ds-1 [585 kB] 138s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.21-1 [690 kB] 138s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el stacks ppc64el 2.68+dfsg-1 [1186 kB] 139s Fetched 3637 kB in 1s (4823 kB/s) 139s Selecting previously unselected package libdbi-perl:ppc64el. 139s (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 ... 106313 files and directories currently installed.) 139s Preparing to unpack .../0-libdbi-perl_1.647-1_ppc64el.deb ... 139s Unpacking libdbi-perl:ppc64el (1.647-1) ... 139s Selecting previously unselected package libdeflate0:ppc64el. 139s Preparing to unpack .../1-libdeflate0_1.23-1_ppc64el.deb ... 139s Unpacking libdeflate0:ppc64el (1.23-1) ... 139s Selecting previously unselected package libgomp1:ppc64el. 139s Preparing to unpack .../2-libgomp1_14.2.0-17ubuntu1_ppc64el.deb ... 139s Unpacking libgomp1:ppc64el (14.2.0-17ubuntu1) ... 139s Selecting previously unselected package libhtscodecs2:ppc64el. 139s Preparing to unpack .../3-libhtscodecs2_1.6.1-1_ppc64el.deb ... 139s Unpacking libhtscodecs2:ppc64el (1.6.1-1) ... 139s Selecting previously unselected package libhts3t64:ppc64el. 139s Preparing to unpack .../4-libhts3t64_1.21+ds-1_ppc64el.deb ... 139s Unpacking libhts3t64:ppc64el (1.21+ds-1) ... 139s Selecting previously unselected package samtools. 139s Preparing to unpack .../5-samtools_1.21-1_ppc64el.deb ... 139s Unpacking samtools (1.21-1) ... 139s Selecting previously unselected package stacks. 139s Preparing to unpack .../6-stacks_2.68+dfsg-1_ppc64el.deb ... 139s Unpacking stacks (2.68+dfsg-1) ... 139s Setting up libhtscodecs2:ppc64el (1.6.1-1) ... 139s Setting up libdeflate0:ppc64el (1.23-1) ... 139s Setting up libgomp1:ppc64el (14.2.0-17ubuntu1) ... 139s Setting up libhts3t64:ppc64el (1.21+ds-1) ... 139s Setting up libdbi-perl:ppc64el (1.647-1) ... 139s Setting up samtools (1.21-1) ... 139s Setting up stacks (2.68+dfsg-1) ... 139s Processing triggers for man-db (2.13.0-1) ... 139s Processing triggers for libc-bin (2.41-1ubuntu1) ... 140s autopkgtest [22:50:40]: test run-unit-test: [----------------------- 140s Stacks - a pipeline for building loci from short-read sequences 140s v2.68+dfsg http://creskolab.uoregon.edu/stacks/ 140s 140s This is the Stacks wrapper script for Debian. Usage: 140s stacks 140s 140s Programs available are: 140s clone_filter ref_map 140s cstacks sstacks 140s denovo_map stacks-dist-extract 140s gstacks stacks-gdb 140s kmer_filter stacks-integrate-alignments 140s phasedstacks stacks-private-alleles 140s populations stacks-samtools-tview 140s process_radtags tsv2bam 140s process_shortreads ustacks 140s 140s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 140s 140s clone_filter 2.68 140s clone_filter [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -o out_dir [-i type] [-y type] [-D] [-h] 140s f: path to the input file if processing single-end sequences. 140s p: path to a directory of files. 140s P: files contained within directory specified by '-p' are paired. 140s 1: first input file in a set of paired-end sequences. 140s 2: second input file in a set of paired-end sequences. 140s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 140s o: path to output the processed files. 140s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 140s D: capture discarded reads to a file. 140s h: display this help message. 140s --oligo-len-1 len: length of the single-end oligo sequence in data set. 140s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 140s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 140s 140s Oligo sequence options: 140s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 140s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 140s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 140s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 140s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 140s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 140s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 140s --index-inline: random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data). 140s 140s cstacks 2.68 140s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 140s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 140s 140s -P,--in-path: path to the directory containing Stacks files. 140s -M,--popmap: path to a population map file. 140s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 140s -t,--threads: enable parallel execution with num_threads threads. 140s -s: sample prefix from which to load loci into the catalog. 140s -o,--outpath: output path to write results. 140s -c,--catalog : add to an existing catalog. 140s 140s Gapped assembly options: 140s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 140s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 140s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 140s 140s Advanced options: 140s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 140s --report-mmatches: report query loci that match more than one catalog locus. 140s denovo_map.pl 2.68 140s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 140s 140s Input/Output files: 140s --samples: path to the directory containing the reads files for each sample. 140s --popmap: path to a population map file (format is " TAB ", one sample per line). 140s -o,--out-path: path to an output directory. 140s 140s General options: 140s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 140s -T, --threads: the number of threads/CPUs to use (default: 1). 140s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 140s --resume: resume executing the pipeline from a previous run. 140s 140s Stack assembly options: 140s -M: number of mismatches allowed between stacks within individuals (for ustacks). 140s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 140s 140s SNP model options: 140s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 140s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 140s 140s Paired-end options: 140s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 140s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 140s the same insert length. 140s 140s Population filtering options: 140s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 140s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 140s 140s For large datasets: 140s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 140s 140s Miscellaneous: 140s --time-components (for benchmarking) 140s gstacks 2.68 140s 140s De novo mode: 140s gstacks -P stacks_dir -M popmap 140s 140s -P: input directory containing '*.matches.bam' files created by the 140s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 140s 140s Reference-based mode: 140s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 140s gstacks -B bam_file [-B ...] -O out_dir 140s 140s -I: input directory containing BAM files 140s -S: with -I/-M, suffix to use to build BAM file names: by default this 140s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 140s -B: input BAM file(s) 140s 140s The input BAM file(s) must be sorted by coordinate. 140s With -B, records must be assigned to samples using BAM "reads groups" 140s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 140s must be consistent if repeated different files. Note that with -I, read 140s groups are unneeded and ignored. 140s 140s For both modes: 140s -M: path to a population map giving the list of samples 140s -O: output directory (default: none with -B; with -P same as the input 140s directory) 140s -t,--threads: number of threads to use (default: 1) 140s 140s SNP Model options: 140s --model: model to use to call variants and genotypes; one of 140s marukilow (default), marukihigh, or snp 140s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 140s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 140s 140s Paired-end options: 140s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 140s have the same insert length (implies --rm-unpaired-reads) 140s --rm-unpaired-reads: discard unpaired reads 140s --ignore-pe-reads: ignore paired-end reads even if present in the input 140s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 140s 140s Advanced options: 140s (De novo mode) 140s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 140s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 140s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 140s --write-alignments: save read alignments (heavy BAM files) 140s 140s (Reference-based mode) 140s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 140s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 140s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 140s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 140s 140s --details: write a heavier output 140s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 140s iterate over when building the graph of allele cooccurrences for 140s SNP phasing (default: 1,2) 140s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 140s genotypes during phasing 140s 140s kmer_filter 2.68 140s kmer_filter [-f in_file_1 [-f in_file_2...] | -p in_dir] [-1 pair_1 -2 pair_2 [-1 pair_1...]] -o out_dir [-i type] [-y type] [-D] [-h] 140s f: path to the input file if processing single-end seqeunces. 140s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 140s p: path to a directory of files (for single-end files only). 140s 1: specify the first in a pair of files to be processed together. 140s 2: specify the second in a pair of files to be processed together. 140s o: path to output the processed files. 140s y: output type, either 'fastq' or 'fasta' (default fastq). 140s D: capture discarded reads to a file. 140s h: display this help message. 140s 140s Filtering options: 140s --rare: turn on filtering based on rare k-mers. 140s --abundant: turn on filtering based on abundant k-mers. 140s --k-len : specify k-mer size (default 15). 140s 140s Advanced filtering options: 140s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 140s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 140s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 140s 140s Normalize data: 140s --normalize : normalize read depth according to k-mer coverage. 140s 140s Characterizing K-mers: 140s --write-k-freq: write kmers along with their frequency of occurrence and exit. 140s --k-dist: print k-mer frequency distribution and exit. 140s 140s Advanced input options: 140s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 140s 140s phasedstacks 2.68 140s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 140s b: Stacks batch ID. 140s P: path to the phased output files. 140s S: path to the Stacks output files. 140s t: input file type. Supported types: fastphase, and beagle. 140s p: number of processes to run in parallel sections of code. 140s M: path to the population map, a tab separated file describing which individuals belong in which population. 140s v: print program version. 140s h: display this help message. 140s --haplotypes: data were phased as RAD locus haplotypes. 140s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 140s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 140s 140s Filtering options: 140s --skip-zeros: do not include D' values of zero in the D' output. 140s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 140s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 140s 140s populations 2.68 140s Usage: 140s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 140s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 140s 140s -P,--in-path: path to a directory containing Stacks output files. 140s -V,--in-vcf: path to a standalone input VCF file. 140s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 140s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 140s -t,--threads: number of threads to run in parallel sections of code. 140s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 140s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 140s 140s Data Filtering: 140s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 140s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 140s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 140s -H,--filter-haplotype-wise: apply the above filters haplotype wise 140s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 140s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 140s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 140s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 140s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 140s 140s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 140s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 140s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 140s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 140s 140s Locus stats: 140s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 140s 140s Fstats: 140s --fstats: enable SNP and haplotype-based F statistics. 140s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 140s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 140s 140s Kernel-smoothing algorithm: 140s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 140s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 140s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 140s (Note: turning on smoothing implies --ordered-export.) 140s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 140s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 140s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 140s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 140s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 140s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 140s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 140s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 140s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 140s 140s File output options: 140s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 140s --fasta-loci: output locus consensus sequences in FASTA format. 140s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 140s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 140s --vcf-all: output all sites in Variant Call Format (VCF). 140s --genepop: output SNPs and haplotypes in GenePop format. 140s --structure: output results in Structure format. 140s --radpainter: output results in fineRADstructure/RADpainter format. 140s --plink: output genotypes in PLINK format. 140s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 140s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 140s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 140s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 140s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 140s --gtf: output locus positions in a GTF annotation file. 140s --no-hap-exports: omit haplotype outputs. 140s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 140s 140s Genetic map output options (population map must specify a genetic cross): 140s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 140s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 140s 140s Additional options: 140s -h,--help: display this help message. 140s -v,--version: print program version. 140s --verbose: turn on additional logging. 140s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 140s process_radtags 2.68 140s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 140s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 140s process_radtags --in-path in_dir [--paired] [--barcodes barcode_file] --out-path out_dir --renz-1 enz [--renz-2 enz] [--threads num] [-c] [-q] [-r] [-t len] 140s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 140s 140s -p,--in-path: path to a directory of files. 140s -P,--paired: files contained within the directory are paired. 140s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 140s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 140s -f: path to the input file if processing single-end sequences. 140s -1: first input file in a set of paired-end sequences. 140s -2: second input file in a set of paired-end sequences. 140s -o,--out-path: path to output the processed files. 140s --basename: specify the prefix of the output files when using -f or -1/-2. 140s 140s --threads: number of threads to run. 140s -c,--clean: clean data, remove any read with an uncalled base ('N'). 140s -q,--quality: discard reads with low quality (phred) scores. 140s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 140s -t,--truncate: truncate final read length to this value. 140s -D,--discards: capture discarded reads to a file. 140s 140s Barcode options: 140s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 140s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 140s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 140s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 140s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 140s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 140s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 140s 140s Restriction enzyme options: 140s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 140s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 140s Currently supported enzymes include: 140s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 140s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 140s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 140s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 140s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 140s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 140s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 140s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 140s 140s Protocol-specific options: 140s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 140s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 140s 140s Adapter options: 140s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 140s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 140s --adapter-mm : number of mismatches allowed in the adapter sequence. 140s 140s Input/Output options: 140s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 140s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 140s --retain-header: retain unmodified FASTQ headers in the output. 140s --merge: if no barcodes are specified, merge all input files into a single output file. 140s 140s Advanced options: 140s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 140s --disable-rad-check: disable checking if the RAD cut site is intact. 140s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 140s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 140s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 140s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 140s --score-limit: set the phred score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 140s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 140s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 140s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 140s process_shortreads 2.68 140s process_shortreads [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir [-i type] [-y type] [-c] [-q] [-r] [-E encoding] [-t len] [-D] [-w size] [-s lim] [-h] 140s f: path to the input file if processing single-end seqeunces. 140s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 140s p: path to a directory of single-end Illumina files. 140s 1: first input file in a set of paired-end sequences. 140s 2: second input file in a set of paired-end sequences. 140s P: specify that input is paired (for use with '-p'). 140s I: specify that the paired-end reads are interleaved in single files. 140s o: path to output the processed files. 140s y: output type, either 'fastq' or 'fasta' (default gzfastq). 140s b: a list of barcodes for this run. 140s c: clean data, remove any read with an uncalled base. 140s q: discard reads with low quality scores. 140s r: rescue barcodes. 140s t: truncate final read length to this value. 140s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 140s D: capture discarded reads to a file. 140s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 140s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 140s h: display this help message. 140s 140s Barcode options: 140s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 140s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 140s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 140s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 140s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 140s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 140s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 140s 140s Adapter options: 140s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 140s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 140s --adapter-mm : number of mismatches allowed in the adapter sequence. 140s 140s Output options: 140s --retain-header: retain unmodified FASTQ headers in the output. 140s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 140s 140s Advanced options: 140s --no-read-trimming: do not trim low quality reads, just discard them. 140s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 140s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 140s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 140s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 140s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 140s ref_map.pl 2.68 140s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 140s 140s Input/Output files: 140s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 140s --popmap: path to a population map file (format is " TAB ", one sample per line). 140s -s: spacer for file names: by default this is empty and the program looks for files 140s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 140s named 'SAMPLE_NAME.SPACER.bam'. 140s -o,--out-path: path to an output directory. 140s 140s General options: 140s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 140s -T: the number of threads/CPUs to use (default: 1). 140s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 140s that would be executed. 140s 140s SNP model options: 140s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 140s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 140s 140s Paired-end options: 140s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 140s the same insert length. 140s --ignore-pe-reads: ignore paired-end reads even if present in the input 140s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 140s 140s Population filtering options: 140s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 140s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 140s 140s Miscellaneous: 140s --time-components (for benchmarking) 140s sstacks 2.68 140s sstacks -P dir -M popmap [-t n_threads] 140s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 140s -P,--in-path: path to the directory containing Stacks files. 140s -M,--popmap: path to a population map file from which to take sample names. 140s -s,--sample: filename prefix from which to load sample loci. 140s -c,--catalog: path to the catalog. 140s -t,--threads: enable parallel execution with n_threads threads. 140s -o,--out-path: output path to write results. 140s -x: don't verify haplotype of matching locus. 140s 140s Gapped assembly options: 140s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 141s usage: 141s stacks-dist-extract logfile [section] 141s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 141s cat logfile | stacks-dist-extract [--pretty] [--section section] 141s 141s Export a paricular section of a Stacks log or distribs file. If you supply a 141s log path alone, stacks-dist-extract will print the available sections to 141s output. The log file can also be supplied via stdin. 141s 141s options: 141s -h, --help show this help message and exit 141s -p, --pretty Output data as a table with columns lined up. 141s -o, --out-path path Path to output file. 141s -s, --section section 141s Name of section to output from the log file. 141s Usage: 141s stacks-gdb PROGRAM ARGUMENTS 141s 141s e.g. 141s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 141s 141s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 141s case of a crash it will print additional information, helping us in fixing the 141s crash. 141s 141s This utility requires GDB, the GNU Debugger, to be installed on the system where 141s Stacks is run. You can check whether this is the case by just typing: 141s 141s gdb --version 141s 141s at the command prompt. Note that you may need to load the corresponding module. 141s GDB is standard scientific software, but may not be installed on some systems. 141s For further information please contact the administrators of your system; 141s trying to install GDB without administrator priviledges is not recommended. 141s 141s For questions please contact us, e.g. at stacks-users@googlegroups.com 141s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 141s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 141s [--version] 141s 141s Extracts the coordinates of the RAD loci from the given BAM file into a 141s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 141s 'catalog.calls' files so that they include the genomic coordinates given in 141s the input BAM file. 141s 141s options: 141s -h, --help show this help message and exit 141s -P, --in-path path Path to a directory containing Stacks ouput files. 141s -B, --bam-path path Path to a SAM or BAM file containing alignment of de 141s novo catalog loci to a reference genome. 141s -O, --out-path path Path to write the integrated ouput files. 141s -q, --min_mapq MIN_MAPQ 141s Minimum mapping quality as listed in the BAM file 141s (default 20). 141s -a, --min_alncov MIN_ALNCOV 141s Minimum fraction of the de novo catalog locus that 141s must participate in the alignment (default 0.6). 141s -p, --min_pctid MIN_PCTID 141s Minimum BLAST-style percent identity of the largest 141s alignment fragment for a de novo catalog locus 141s (default 0.6). 141s --verbose Provide verbose output. 141s --version show program's version number and exit 141s usage: 141s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 141s 141s Displays the read alignments of the given sample for the given locus, in text 141s format, to the standard output. Requires gstacks to have been run with the 141s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 141s tsv2bam 2.68 141s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 141s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 141s 141s -P,--in-dir: input directory. 141s -M,--popmap: population map. 141s -s,--sample: name of one sample. 141s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 141s -t: number of threads to use (default: 1). 141s 141s ustacks 2.68 141s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 141s -f,--file: input file path. 141s -o,--out-path: output path to write results. 141s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 141s -m: Minimum number of reads to seed a new stack (default 3). 141s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 141s -t,--threads: enable parallel execution with num_threads threads. 141s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 141s -n,--name: a name for the sample (default: input file name minus the suffix). 141s -R: retain unused reads. 141s -H: disable calling haplotypes from secondary reads. 141s 141s Stack assembly options: 141s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 141s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 141s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 141s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 141s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 141s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 141s 141s Gapped assembly options: 141s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 141s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 141s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 141s 141s Model options: 141s --model-type: either 'snp' (default), 'bounded', or 'fixed' 141s For the SNP or Bounded SNP model: 141s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 141s For the Bounded SNP model: 141s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 141s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 141s For the Fixed model: 141s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 141s 141s h: display this help message. 141s autopkgtest [22:50:41]: test run-unit-test: -----------------------] 141s run-unit-test PASS (superficial) 141s autopkgtest [22:50:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 142s autopkgtest [22:50:42]: @@@@@@@@@@@@@@@@@@@@ summary 142s run-unit-test PASS (superficial) 158s nova [W] Using flock in prodstack6-ppc64el 158s Creating nova instance adt-plucky-ppc64el-stacks-20250215-224820-juju-7f2275-prod-proposed-migration-environment-20-c5f3f1bf-165f-41be-b52b-3a952d541982 from image adt/ubuntu-plucky-ppc64el-server-20250215.img (UUID 6b0563e5-c35c-4c0f-8fb5-aae43570455f)... 158s nova [W] Timed out waiting for 9313c82b-cc5c-4951-852d-7c2ea9a0ba9b to get deleted.