0s autopkgtest [03:19:15]: starting date and time: 2025-02-16 03:19:15+0000 0s autopkgtest [03:19:15]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [03:19:15]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y7yqnhaa/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-1.secgroup --name adt-plucky-s390x-stacks-20250216-031915-juju-7f2275-prod-proposed-migration-environment-20-f6696a8b-a4fd-4bc8-840e-ef0979c27cbb --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 103s autopkgtest [03:20:58]: testbed dpkg architecture: s390x 103s autopkgtest [03:20:58]: testbed apt version: 2.9.28 103s autopkgtest [03:20:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s autopkgtest [03:20:58]: testbed release detected to be: None 104s autopkgtest [03:20:59]: updating testbed package index (apt update) 104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [810 kB] 105s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.0 kB] 105s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 105s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 105s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [166 kB] 105s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [760 B] 105s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [855 kB] 105s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3740 B] 105s Fetched 2035 kB in 1s (2048 kB/s) 106s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s The following packages will be REMOVED: 107s linux-image-6.11.0-8-generic* 107s 0 upgraded, 0 newly installed, 1 to remove and 6 not upgraded. 107s After this operation, 10.5 MB disk space will be freed. 107s (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 ... 80973 files and directories currently installed.) 107s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 107s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-15-generic 107s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-15-generic 107s /etc/kernel/postrm.d/initramfs-tools: 107s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 107s /etc/kernel/postrm.d/zz-zipl: 107s Using config file '/etc/zipl.conf' 107s Building bootmap in '/boot' 107s Adding IPL section 'ubuntu' (default) 107s Preparing boot device for LD-IPL: vda (0000). 107s Done. 107s (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 ... 80969 files and directories currently installed.) 107s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 107s rmdir: failed to remove '/lib/modules/6.11.0-8-generic': Directory not empty 108s autopkgtest [03:21:03]: upgrading testbed (apt dist-upgrade and autopurge) 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 108s Entering ResolveByKeep 108s 109s The following packages were automatically installed and are no longer required: 109s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 109s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 109s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 109s linux-tools-6.11.0-8-generic 109s Use 'sudo apt autoremove' to remove them. 109s The following packages will be upgraded: 109s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 109s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 10.7 MB of archives. 109s After this operation, 305 kB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu1 [24.3 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu1 [1679 kB] 109s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu1 [4246 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu1 [2891 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu1 [672 kB] 109s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x iproute2 s390x 6.13.0-1ubuntu1 [1174 kB] 110s Preconfiguring packages ... 110s Fetched 10.7 MB in 1s (12.4 MB/s) 110s (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 ... 80969 files and directories currently installed.) 110s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_s390x.deb ... 110s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 110s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_s390x.deb ... 110s Unpacking libc6-dev:s390x (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 110s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 110s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 110s Preparing to unpack .../libc6_2.41-1ubuntu1_s390x.deb ... 110s Checking for services that may need to be restarted... 110s Checking init scripts... 110s Checking for services that may need to be restarted... 110s Checking init scripts... 110s Stopping some services possibly affected by the upgrade (will be restarted later): 110s cron: stopping...done. 110s 110s Unpacking libc6:s390x (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 110s Setting up libc6:s390x (2.41-1ubuntu1) ... 110s Checking for services that may need to be restarted... 110s Checking init scripts... 110s Restarting services possibly affected by the upgrade: 110s cron: restarting...done. 110s 110s Services restarted successfully. 110s (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 ... 80970 files and directories currently installed.) 110s Preparing to unpack .../libc-bin_2.41-1ubuntu1_s390x.deb ... 110s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 110s Setting up libc-bin (2.41-1ubuntu1) ... 110s (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 ... 80970 files and directories currently installed.) 110s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_s390x.deb ... 111s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 111s Setting up iproute2 (6.13.0-1ubuntu1) ... 111s Setting up locales (2.41-1ubuntu1) ... 111s Installing new version of config file /etc/locale.alias ... 111s Generating locales (this might take a while)... 112s en_US.UTF-8... done 112s Generation complete. 112s Setting up libc-dev-bin (2.41-1ubuntu1) ... 112s Setting up libc6-dev:s390x (2.41-1ubuntu1) ... 112s Processing triggers for man-db (2.13.0-1) ... 113s Processing triggers for systemd (257.2-3ubuntu1) ... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Starting pkgProblemResolver with broken count: 0 114s Starting 2 pkgProblemResolver with broken count: 0 114s Done 114s The following packages will be REMOVED: 114s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 114s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 114s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 114s linux-tools-6.11.0-8-generic* 114s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 114s After this operation, 167 MB disk space will be freed. 114s (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 ... 80971 files and directories currently installed.) 114s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 114s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 114s Removing libpython3.12t64:s390x (3.12.9-1) ... 114s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 114s Removing libnsl2:s390x (1.3.0-3build3) ... 114s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 115s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 115s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 115s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 115s Processing triggers for libc-bin (2.41-1ubuntu1) ... 115s (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 ... 55871 files and directories currently installed.) 115s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 115s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 116s autopkgtest [03:21:11]: rebooting testbed after setup commands that affected boot 135s autopkgtest [03:21:30]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 15:05:57 UTC 2025 137s autopkgtest [03:21:32]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 138s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (dsc) [2070 B] 138s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (tar) [371 kB] 138s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (diff) [12.2 kB] 139s gpgv: Signature made Sat Aug 31 10:00:49 2024 UTC 139s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 139s gpgv: issuer "emollier@debian.org" 139s gpgv: Can't check signature: No public key 139s dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-1.dsc: no acceptable signature found 139s autopkgtest [03:21:34]: testing package stacks version 2.68+dfsg-1 139s autopkgtest [03:21:34]: build not needed 140s autopkgtest [03:21:35]: test run-unit-test: preparing testbed 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Starting pkgProblemResolver with broken count: 0 140s Starting 2 pkgProblemResolver with broken count: 0 140s Done 140s The following NEW packages will be installed: 140s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 140s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 3404 kB of archives. 140s After this operation, 9750 kB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libdbi-perl s390x 1.647-1 [832 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-17ubuntu1 [151 kB] 141s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-1 [91.1 kB] 141s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x samtools s390x 1.21-1 [633 kB] 141s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x stacks s390x 2.68+dfsg-1 [1171 kB] 141s Fetched 3404 kB in 1s (5039 kB/s) 141s Selecting previously unselected package libdbi-perl:s390x. 141s (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 ... 55869 files and directories currently installed.) 141s Preparing to unpack .../0-libdbi-perl_1.647-1_s390x.deb ... 141s Unpacking libdbi-perl:s390x (1.647-1) ... 141s Selecting previously unselected package libdeflate0:s390x. 141s Preparing to unpack .../1-libdeflate0_1.23-1_s390x.deb ... 141s Unpacking libdeflate0:s390x (1.23-1) ... 141s Selecting previously unselected package libgomp1:s390x. 141s Preparing to unpack .../2-libgomp1_14.2.0-17ubuntu1_s390x.deb ... 141s Unpacking libgomp1:s390x (14.2.0-17ubuntu1) ... 141s Selecting previously unselected package libhtscodecs2:s390x. 141s Preparing to unpack .../3-libhtscodecs2_1.6.1-1_s390x.deb ... 141s Unpacking libhtscodecs2:s390x (1.6.1-1) ... 141s Selecting previously unselected package libhts3t64:s390x. 141s Preparing to unpack .../4-libhts3t64_1.21+ds-1_s390x.deb ... 141s Unpacking libhts3t64:s390x (1.21+ds-1) ... 141s Selecting previously unselected package samtools. 141s Preparing to unpack .../5-samtools_1.21-1_s390x.deb ... 141s Unpacking samtools (1.21-1) ... 141s Selecting previously unselected package stacks. 141s Preparing to unpack .../6-stacks_2.68+dfsg-1_s390x.deb ... 141s Unpacking stacks (2.68+dfsg-1) ... 141s Setting up libhtscodecs2:s390x (1.6.1-1) ... 141s Setting up libdeflate0:s390x (1.23-1) ... 141s Setting up libgomp1:s390x (14.2.0-17ubuntu1) ... 141s Setting up libhts3t64:s390x (1.21+ds-1) ... 141s Setting up libdbi-perl:s390x (1.647-1) ... 141s Setting up samtools (1.21-1) ... 141s Setting up stacks (2.68+dfsg-1) ... 141s Processing triggers for man-db (2.13.0-1) ... 142s Processing triggers for libc-bin (2.41-1ubuntu1) ... 143s autopkgtest [03:21:38]: test run-unit-test: [----------------------- 143s Stacks - a pipeline for building loci from short-read sequences 143s v2.68+dfsg http://creskolab.uoregon.edu/stacks/ 143s 143s This is the Stacks wrapper script for Debian. Usage: 143s stacks 143s 143s Programs available are: 143s clone_filter ref_map 143s cstacks sstacks 143s denovo_map stacks-dist-extract 143s gstacks stacks-gdb 143s kmer_filter stacks-integrate-alignments 143s phasedstacks stacks-private-alleles 143s populations stacks-samtools-tview 143s process_radtags tsv2bam 143s process_shortreads ustacks 143s 143s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 143s 143s clone_filter 2.68 143s 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] 143s f: path to the input file if processing single-end sequences. 143s p: path to a directory of files. 143s P: files contained within directory specified by '-p' are paired. 143s 1: first input file in a set of paired-end sequences. 143s 2: second input file in a set of paired-end sequences. 143s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 143s o: path to output the processed files. 143s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 143s D: capture discarded reads to a file. 143s h: display this help message. 143s --oligo-len-1 len: length of the single-end oligo sequence in data set. 143s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 143s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 143s 143s Oligo sequence options: 143s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 143s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 143s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 143s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 143s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 143s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 143s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 143s --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). 143s 143s cstacks 2.68 143s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 143s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 143s 143s -P,--in-path: path to the directory containing Stacks files. 143s -M,--popmap: path to a population map file. 143s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 143s -t,--threads: enable parallel execution with num_threads threads. 143s -s: sample prefix from which to load loci into the catalog. 143s -o,--outpath: output path to write results. 143s -c,--catalog : add to an existing catalog. 143s 143s Gapped assembly options: 143s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 143s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 143s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 143s 143s Advanced options: 143s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 143s --report-mmatches: report query loci that match more than one catalog locus. 143s denovo_map.pl 2.68 143s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 143s 143s Input/Output files: 143s --samples: path to the directory containing the reads files for each sample. 143s --popmap: path to a population map file (format is " TAB ", one sample per line). 143s -o,--out-path: path to an output directory. 143s 143s General options: 143s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 143s -T, --threads: the number of threads/CPUs to use (default: 1). 143s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 143s --resume: resume executing the pipeline from a previous run. 143s 143s Stack assembly options: 143s -M: number of mismatches allowed between stacks within individuals (for ustacks). 143s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 143s 143s SNP model options: 143s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 143s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 143s 143s Paired-end options: 143s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 143s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 143s the same insert length. 143s 143s Population filtering options: 143s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 143s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 143s 143s For large datasets: 143s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 143s 143s Miscellaneous: 143s --time-components (for benchmarking) 143s gstacks 2.68 143s 143s De novo mode: 143s gstacks -P stacks_dir -M popmap 143s 143s -P: input directory containing '*.matches.bam' files created by the 143s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 143s 143s Reference-based mode: 143s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 143s gstacks -B bam_file [-B ...] -O out_dir 143s 143s -I: input directory containing BAM files 143s -S: with -I/-M, suffix to use to build BAM file names: by default this 143s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 143s -B: input BAM file(s) 143s 143s The input BAM file(s) must be sorted by coordinate. 143s With -B, records must be assigned to samples using BAM "reads groups" 143s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 143s must be consistent if repeated different files. Note that with -I, read 143s groups are unneeded and ignored. 143s 143s For both modes: 143s -M: path to a population map giving the list of samples 143s -O: output directory (default: none with -B; with -P same as the input 143s directory) 143s -t,--threads: number of threads to use (default: 1) 143s 143s SNP Model options: 143s --model: model to use to call variants and genotypes; one of 143s marukilow (default), marukihigh, or snp 143s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 143s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 143s 143s Paired-end options: 143s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 143s have the same insert length (implies --rm-unpaired-reads) 143s --rm-unpaired-reads: discard unpaired reads 143s --ignore-pe-reads: ignore paired-end reads even if present in the input 143s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 143s 143s Advanced options: 143s (De novo mode) 143s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 143s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 143s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 143s --write-alignments: save read alignments (heavy BAM files) 143s 143s (Reference-based mode) 143s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 143s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 143s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 143s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 143s 143s --details: write a heavier output 143s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 143s iterate over when building the graph of allele cooccurrences for 143s SNP phasing (default: 1,2) 143s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 143s genotypes during phasing 143s 143s kmer_filter 2.68 143s 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] 143s f: path to the input file if processing single-end seqeunces. 143s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 143s p: path to a directory of files (for single-end files only). 143s 1: specify the first in a pair of files to be processed together. 143s 2: specify the second in a pair of files to be processed together. 143s o: path to output the processed files. 143s y: output type, either 'fastq' or 'fasta' (default fastq). 143s D: capture discarded reads to a file. 143s h: display this help message. 143s 143s Filtering options: 143s --rare: turn on filtering based on rare k-mers. 143s --abundant: turn on filtering based on abundant k-mers. 143s --k-len : specify k-mer size (default 15). 143s 143s Advanced filtering options: 143s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 143s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 143s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 143s 143s Normalize data: 143s --normalize : normalize read depth according to k-mer coverage. 143s 143s Characterizing K-mers: 143s --write-k-freq: write kmers along with their frequency of occurrence and exit. 143s --k-dist: print k-mer frequency distribution and exit. 143s 143s Advanced input options: 143s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 143s 143s phasedstacks 2.68 143s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 143s b: Stacks batch ID. 143s P: path to the phased output files. 143s S: path to the Stacks output files. 143s t: input file type. Supported types: fastphase, and beagle. 143s p: number of processes to run in parallel sections of code. 143s M: path to the population map, a tab separated file describing which individuals belong in which population. 143s v: print program version. 143s h: display this help message. 143s --haplotypes: data were phased as RAD locus haplotypes. 143s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 143s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 143s 143s Filtering options: 143s --skip-zeros: do not include D' values of zero in the D' output. 143s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 143s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 143s 143s populations 2.68 143s Usage: 143s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 143s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 143s 143s -P,--in-path: path to a directory containing Stacks output files. 143s -V,--in-vcf: path to a standalone input VCF file. 143s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 143s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 143s -t,--threads: number of threads to run in parallel sections of code. 143s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 143s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 143s 143s Data Filtering: 143s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 143s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 143s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 143s -H,--filter-haplotype-wise: apply the above filters haplotype wise 143s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 143s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 143s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 143s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 143s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 143s 143s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 143s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 143s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 143s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 143s 143s Locus stats: 143s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 143s 143s Fstats: 143s --fstats: enable SNP and haplotype-based F statistics. 143s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 143s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 143s 143s Kernel-smoothing algorithm: 143s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 143s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 143s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 143s (Note: turning on smoothing implies --ordered-export.) 143s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 143s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 143s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 143s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 143s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 143s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 143s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 143s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 143s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 143s 143s File output options: 143s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 143s --fasta-loci: output locus consensus sequences in FASTA format. 143s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 143s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 143s --vcf-all: output all sites in Variant Call Format (VCF). 143s --genepop: output SNPs and haplotypes in GenePop format. 143s --structure: output results in Structure format. 143s --radpainter: output results in fineRADstructure/RADpainter format. 143s --plink: output genotypes in PLINK format. 143s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 143s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 143s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 143s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 143s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 143s --gtf: output locus positions in a GTF annotation file. 143s --no-hap-exports: omit haplotype outputs. 143s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 143s 143s Genetic map output options (population map must specify a genetic cross): 143s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 143s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 143s 143s Additional options: 143s -h,--help: display this help message. 143s -v,--version: print program version. 143s --verbose: turn on additional logging. 143s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 143s process_radtags 2.68 143s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 143s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 143s 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] 143s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 143s 143s -p,--in-path: path to a directory of files. 143s -P,--paired: files contained within the directory are paired. 143s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 143s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 143s -f: path to the input file if processing single-end sequences. 143s -1: first input file in a set of paired-end sequences. 143s -2: second input file in a set of paired-end sequences. 143s -o,--out-path: path to output the processed files. 143s --basename: specify the prefix of the output files when using -f or -1/-2. 143s 143s --threads: number of threads to run. 143s -c,--clean: clean data, remove any read with an uncalled base ('N'). 143s -q,--quality: discard reads with low quality (phred) scores. 143s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 143s -t,--truncate: truncate final read length to this value. 143s -D,--discards: capture discarded reads to a file. 143s 143s Barcode options: 143s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 143s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 143s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 143s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 143s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 143s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 143s --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). 143s 143s Restriction enzyme options: 143s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 143s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 143s Currently supported enzymes include: 143s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 143s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 143s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 143s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 143s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 143s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 143s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 143s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 143s 143s Protocol-specific options: 143s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 143s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 143s 143s Adapter options: 143s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 143s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 143s --adapter-mm : number of mismatches allowed in the adapter sequence. 143s 143s Input/Output options: 143s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 143s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 143s --retain-header: retain unmodified FASTQ headers in the output. 143s --merge: if no barcodes are specified, merge all input files into a single output file. 143s 143s Advanced options: 143s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 143s --disable-rad-check: disable checking if the RAD cut site is intact. 143s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 143s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 143s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 143s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 143s --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). 143s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 143s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 143s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 143s process_shortreads 2.68 143s 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] 143s f: path to the input file if processing single-end seqeunces. 143s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 143s p: path to a directory of single-end Illumina files. 143s 1: first input file in a set of paired-end sequences. 143s 2: second input file in a set of paired-end sequences. 143s P: specify that input is paired (for use with '-p'). 143s I: specify that the paired-end reads are interleaved in single files. 143s o: path to output the processed files. 143s y: output type, either 'fastq' or 'fasta' (default gzfastq). 143s b: a list of barcodes for this run. 143s c: clean data, remove any read with an uncalled base. 143s q: discard reads with low quality scores. 143s r: rescue barcodes. 143s t: truncate final read length to this value. 143s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 143s D: capture discarded reads to a file. 143s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 143s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 143s h: display this help message. 143s 143s Barcode options: 143s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 143s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 143s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 143s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 143s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 143s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 143s --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). 143s 143s Adapter options: 143s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 143s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 143s --adapter-mm : number of mismatches allowed in the adapter sequence. 143s 143s Output options: 143s --retain-header: retain unmodified FASTQ headers in the output. 143s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 143s 143s Advanced options: 143s --no-read-trimming: do not trim low quality reads, just discard them. 143s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 143s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 143s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 143s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 143s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 143s ref_map.pl 2.68 143s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 143s 143s Input/Output files: 143s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 143s --popmap: path to a population map file (format is " TAB ", one sample per line). 143s -s: spacer for file names: by default this is empty and the program looks for files 143s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 143s named 'SAMPLE_NAME.SPACER.bam'. 143s -o,--out-path: path to an output directory. 143s 143s General options: 143s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 143s -T: the number of threads/CPUs to use (default: 1). 143s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 143s that would be executed. 143s 143s SNP model options: 143s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 143s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 143s 143s Paired-end options: 143s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 143s the same insert length. 143s --ignore-pe-reads: ignore paired-end reads even if present in the input 143s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 143s 143s Population filtering options: 143s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 143s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 143s 143s Miscellaneous: 143s --time-components (for benchmarking) 143s sstacks 2.68 143s sstacks -P dir -M popmap [-t n_threads] 143s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 143s -P,--in-path: path to the directory containing Stacks files. 143s -M,--popmap: path to a population map file from which to take sample names. 143s -s,--sample: filename prefix from which to load sample loci. 143s -c,--catalog: path to the catalog. 143s -t,--threads: enable parallel execution with n_threads threads. 143s -o,--out-path: output path to write results. 143s -x: don't verify haplotype of matching locus. 143s 143s Gapped assembly options: 143s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 143s usage: 143s stacks-dist-extract logfile [section] 143s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 143s cat logfile | stacks-dist-extract [--pretty] [--section section] 143s 143s Export a paricular section of a Stacks log or distribs file. If you supply a 143s log path alone, stacks-dist-extract will print the available sections to 143s output. The log file can also be supplied via stdin. 143s 143s options: 143s -h, --help show this help message and exit 143s -p, --pretty Output data as a table with columns lined up. 143s -o, --out-path path Path to output file. 143s -s, --section section 143s Name of section to output from the log file. 143s Usage: 143s stacks-gdb PROGRAM ARGUMENTS 143s 143s e.g. 143s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 143s 143s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 143s case of a crash it will print additional information, helping us in fixing the 143s crash. 143s 143s This utility requires GDB, the GNU Debugger, to be installed on the system where 143s Stacks is run. You can check whether this is the case by just typing: 143s 143s gdb --version 143s 143s at the command prompt. Note that you may need to load the corresponding module. 143s GDB is standard scientific software, but may not be installed on some systems. 143s For further information please contact the administrators of your system; 143s trying to install GDB without administrator priviledges is not recommended. 143s 143s For questions please contact us, e.g. at stacks-users@googlegroups.com 143s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 143s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 143s [--version] 143s 143s Extracts the coordinates of the RAD loci from the given BAM file into a 143s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 143s 'catalog.calls' files so that they include the genomic coordinates given in 143s the input BAM file. 143s 143s options: 143s -h, --help show this help message and exit 143s -P, --in-path path Path to a directory containing Stacks ouput files. 143s -B, --bam-path path Path to a SAM or BAM file containing alignment of de 143s novo catalog loci to a reference genome. 143s -O, --out-path path Path to write the integrated ouput files. 143s -q, --min_mapq MIN_MAPQ 143s Minimum mapping quality as listed in the BAM file 143s (default 20). 143s -a, --min_alncov MIN_ALNCOV 143s Minimum fraction of the de novo catalog locus that 143s must participate in the alignment (default 0.6). 143s -p, --min_pctid MIN_PCTID 143s Minimum BLAST-style percent identity of the largest 143s alignment fragment for a de novo catalog locus 143s (default 0.6). 143s --verbose Provide verbose output. 143s --version show program's version number and exit 143s usage: 143s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 143s 143s Displays the read alignments of the given sample for the given locus, in text 143s format, to the standard output. Requires gstacks to have been run with the 143s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 143s tsv2bam 2.68 143s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 143s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 143s 143s -P,--in-dir: input directory. 143s -M,--popmap: population map. 143s -s,--sample: name of one sample. 143s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 143s -t: number of threads to use (default: 1). 143s 143s ustacks 2.68 143s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 143s -f,--file: input file path. 143s -o,--out-path: output path to write results. 143s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 143s -m: Minimum number of reads to seed a new stack (default 3). 143s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 143s -t,--threads: enable parallel execution with num_threads threads. 143s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 143s -n,--name: a name for the sample (default: input file name minus the suffix). 143s -R: retain unused reads. 143s -H: disable calling haplotypes from secondary reads. 143s 143s Stack assembly options: 143s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 143s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 143s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 143s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 143s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 143s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 143s 143s Gapped assembly options: 143s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 143s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 143s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 143s 143s Model options: 143s --model-type: either 'snp' (default), 'bounded', or 'fixed' 143s For the SNP or Bounded SNP model: 143s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 143s For the Bounded SNP model: 143s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 143s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 143s For the Fixed model: 143s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 143s 143s h: display this help message. 143s autopkgtest [03:21:38]: test run-unit-test: -----------------------] 144s autopkgtest [03:21:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 144s run-unit-test PASS (superficial) 144s autopkgtest [03:21:39]: @@@@@@@@@@@@@@@@@@@@ summary 144s run-unit-test PASS (superficial) 161s nova [W] Using flock in prodstack6-s390x 161s flock: timeout while waiting to get lock 161s Creating nova instance adt-plucky-s390x-stacks-20250216-031915-juju-7f2275-prod-proposed-migration-environment-20-f6696a8b-a4fd-4bc8-840e-ef0979c27cbb from image adt/ubuntu-plucky-s390x-server-20250216.img (UUID 67327349-c50d-4fb2-aab8-abef6582e685)... 161s nova [W] Timed out waiting for ced26d79-2340-4598-a79a-69ab5a4a8127 to get deleted.