0s autopkgtest [16:56:41]: starting date and time: 2025-03-15 16:56:41+0000 0s autopkgtest [16:56:41]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:56:41]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bpimiz1u/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade stacks --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-40.secgroup --name adt-plucky-arm64-stacks-20250315-165641-juju-7f2275-prod-proposed-migration-environment-20-25e36112-84c7-40ba-a6e4-2307be00e4b9 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -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/ 152s autopkgtest [16:59:13]: testbed dpkg architecture: arm64 153s autopkgtest [16:59:14]: testbed apt version: 2.9.33 153s autopkgtest [16:59:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 153s autopkgtest [16:59:14]: testbed release detected to be: None 154s autopkgtest [16:59:15]: updating testbed package index (apt update) 154s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 155s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 155s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 155s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 155s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 155s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 155s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 155s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 155s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 155s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 155s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 156s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 156s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 156s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 156s Fetched 1078 kB in 2s (698 kB/s) 157s Reading package lists... 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s Calculating upgrade... 159s Calculating upgrade... 159s The following packages will be upgraded: 159s pinentry-curses python3-jinja2 strace 159s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 647 kB of archives. 159s After this operation, 11.3 kB of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 160s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 161s Fetched 647 kB in 1s (505 kB/s) 161s (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 ... 117701 files and directories currently installed.) 161s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 161s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 161s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 161s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 162s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 162s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 162s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 162s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 162s Setting up strace (6.13+ds-1ubuntu1) ... 162s Processing triggers for man-db (2.13.0-1) ... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Solving dependencies... 164s The following packages will be REMOVED: 164s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 164s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 164s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 164s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 164s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 164s After this operation, 267 MB disk space will be freed. 164s (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 ... 117701 files and directories currently installed.) 164s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 164s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 164s Removing libpython3.12t64:arm64 (3.12.9-1) ... 164s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 165s Removing libnsl2:arm64 (1.3.0-3build3) ... 165s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 165s Removing libunwind8:arm64 (1.6.2-3.1) ... 165s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 165s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 167s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 167s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 167s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 167s /etc/kernel/postrm.d/initramfs-tools: 167s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 167s /etc/kernel/postrm.d/zz-flash-kernel: 167s flash-kernel: Kernel 6.11.0-8-generic has been removed. 167s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 168s /etc/kernel/postrm.d/zz-update-grub: 168s Sourcing file `/etc/default/grub' 168s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 168s Generating grub configuration file ... 168s Found linux image: /boot/vmlinuz-6.14.0-10-generic 168s Found initrd image: /boot/initrd.img-6.14.0-10-generic 168s Warning: os-prober will not be executed to detect other bootable partitions. 168s Systems on them will not be added to the GRUB boot configuration. 168s Check GRUB_DISABLE_OS_PROBER documentation entry. 168s Adding boot menu entry for UEFI Firmware Settings ... 168s done 168s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 169s Processing triggers for libc-bin (2.41-1ubuntu1) ... 169s (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 ... 81650 files and directories currently installed.) 169s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 169s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 169s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 169s autopkgtest [16:59:30]: upgrading testbed (apt dist-upgrade and autopurge) 169s Reading package lists... 170s Building dependency tree... 170s Reading state information... 171s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 171s Starting 2 pkgProblemResolver with broken count: 0 171s Done 171s Entering ResolveByKeep 171s 172s Calculating upgrade... 172s The following packages will be upgraded: 172s libc-bin libc-dev-bin libc6 libc6-dev locales 172s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 9530 kB of archives. 172s After this operation, 0 B of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 174s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 177s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 178s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 184s Preconfiguring packages ... 184s Fetched 9530 kB in 12s (805 kB/s) 184s (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 ... 81647 files and directories currently installed.) 184s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 184s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 185s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 185s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 185s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 185s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 185s Setting up libc6:arm64 (2.41-1ubuntu2) ... 185s (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 ... 81647 files and directories currently installed.) 185s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 185s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 185s Setting up libc-bin (2.41-1ubuntu2) ... 185s (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 ... 81647 files and directories currently installed.) 185s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 185s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Setting up locales (2.41-1ubuntu2) ... 187s Generating locales (this might take a while)... 189s en_US.UTF-8... done 189s Generation complete. 189s Setting up libc-dev-bin (2.41-1ubuntu2) ... 189s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 189s Processing triggers for man-db (2.13.0-1) ... 190s Processing triggers for systemd (257.3-1ubuntu3) ... 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 192s Solving dependencies... 192s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s autopkgtest [16:59:53]: rebooting testbed after setup commands that affected boot 217s autopkgtest [17:00:18]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 220s autopkgtest [17:00:21]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 223s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (dsc) [2050 B] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (tar) [371 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (diff) [12.5 kB] 223s gpgv: Signature made Sun Feb 16 10:21:57 2025 UTC 223s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 223s gpgv: issuer "emollier@debian.org" 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-2.dsc: no acceptable signature found 223s autopkgtest [17:00:24]: testing package stacks version 2.68+dfsg-2 223s autopkgtest [17:00:24]: build not needed 224s autopkgtest [17:00:25]: test run-unit-test: preparing testbed 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 226s The following NEW packages will be installed: 226s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 226s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 3190 kB of archives. 226s After this operation, 10.1 MB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libdbi-perl arm64 1.647-1 [827 kB] 228s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 228s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 228s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 228s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 229s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB] 229s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 stacks arm64 2.68+dfsg-2 [1038 kB] 231s Fetched 3190 kB in 5s (606 kB/s) 232s Selecting previously unselected package libdbi-perl:arm64. 232s (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 ... 81647 files and directories currently installed.) 232s Preparing to unpack .../0-libdbi-perl_1.647-1_arm64.deb ... 232s Unpacking libdbi-perl:arm64 (1.647-1) ... 232s Selecting previously unselected package libdeflate0:arm64. 232s Preparing to unpack .../1-libdeflate0_1.23-1_arm64.deb ... 232s Unpacking libdeflate0:arm64 (1.23-1) ... 232s Selecting previously unselected package libgomp1:arm64. 232s Preparing to unpack .../2-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 232s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 232s Selecting previously unselected package libhtscodecs2:arm64. 232s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_arm64.deb ... 232s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 232s Selecting previously unselected package libhts3t64:arm64. 232s Preparing to unpack .../4-libhts3t64_1.21+ds-1_arm64.deb ... 232s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 232s Selecting previously unselected package samtools. 232s Preparing to unpack .../5-samtools_1.21-1_arm64.deb ... 232s Unpacking samtools (1.21-1) ... 232s Selecting previously unselected package stacks. 232s Preparing to unpack .../6-stacks_2.68+dfsg-2_arm64.deb ... 232s Unpacking stacks (2.68+dfsg-2) ... 232s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 232s Setting up libdeflate0:arm64 (1.23-1) ... 232s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 232s Setting up libhts3t64:arm64 (1.21+ds-1) ... 232s Setting up libdbi-perl:arm64 (1.647-1) ... 232s Setting up samtools (1.21-1) ... 232s Setting up stacks (2.68+dfsg-2) ... 232s Processing triggers for man-db (2.13.0-1) ... 233s Processing triggers for libc-bin (2.41-1ubuntu2) ... 234s autopkgtest [17:00:35]: test run-unit-test: [----------------------- 235s Stacks - a pipeline for building loci from short-read sequences 235s v2.68+dfsg http://creskolab.uoregon.edu/stacks/ 235s 235s This is the Stacks wrapper script for Debian. Usage: 235s stacks 235s 235s Programs available are: 235s clone_filter ref_map 235s cstacks sstacks 235s denovo_map stacks-dist-extract 235s gstacks stacks-gdb 235s kmer_filter stacks-integrate-alignments 235s phasedstacks stacks-private-alleles 235s populations stacks-samtools-tview 235s process_radtags tsv2bam 235s process_shortreads ustacks 235s 235s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 235s 235s clone_filter 2.68 235s 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] 235s f: path to the input file if processing single-end sequences. 235s p: path to a directory of files. 235s P: files contained within directory specified by '-p' are paired. 235s 1: first input file in a set of paired-end sequences. 235s 2: second input file in a set of paired-end sequences. 235s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 235s o: path to output the processed files. 235s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 235s D: capture discarded reads to a file. 235s h: display this help message. 235s --oligo-len-1 len: length of the single-end oligo sequence in data set. 235s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 235s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 235s 235s Oligo sequence options: 235s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 235s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 235s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 235s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 235s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 235s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 235s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 235s --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). 235s 235s cstacks 2.68 235s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 235s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 235s 235s -P,--in-path: path to the directory containing Stacks files. 235s -M,--popmap: path to a population map file. 235s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 235s -t,--threads: enable parallel execution with num_threads threads. 235s -s: sample prefix from which to load loci into the catalog. 235s -o,--outpath: output path to write results. 235s -c,--catalog : add to an existing catalog. 235s 235s Gapped assembly options: 235s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 235s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 235s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 235s 235s Advanced options: 235s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 235s --report-mmatches: report query loci that match more than one catalog locus. 235s denovo_map.pl 2.68 235s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 235s 235s Input/Output files: 235s --samples: path to the directory containing the reads files for each sample. 235s --popmap: path to a population map file (format is " TAB ", one sample per line). 235s -o,--out-path: path to an output directory. 235s 235s General options: 235s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 235s -T, --threads: the number of threads/CPUs to use (default: 1). 235s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 235s --resume: resume executing the pipeline from a previous run. 235s 235s Stack assembly options: 235s -M: number of mismatches allowed between stacks within individuals (for ustacks). 235s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 235s 235s SNP model options: 235s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 235s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 235s 235s Paired-end options: 235s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 235s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 235s the same insert length. 235s 235s Population filtering options: 235s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 235s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 235s 235s For large datasets: 235s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 235s 235s Miscellaneous: 235s --time-components (for benchmarking) 235s gstacks 2.68 235s 235s De novo mode: 235s gstacks -P stacks_dir -M popmap 235s 235s -P: input directory containing '*.matches.bam' files created by the 235s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 235s 235s Reference-based mode: 235s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 235s gstacks -B bam_file [-B ...] -O out_dir 235s 235s -I: input directory containing BAM files 235s -S: with -I/-M, suffix to use to build BAM file names: by default this 235s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 235s -B: input BAM file(s) 235s 235s The input BAM file(s) must be sorted by coordinate. 235s With -B, records must be assigned to samples using BAM "reads groups" 235s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 235s must be consistent if repeated different files. Note that with -I, read 235s groups are unneeded and ignored. 235s 235s For both modes: 235s -M: path to a population map giving the list of samples 235s -O: output directory (default: none with -B; with -P same as the input 235s directory) 235s -t,--threads: number of threads to use (default: 1) 235s 235s SNP Model options: 235s --model: model to use to call variants and genotypes; one of 235s marukilow (default), marukihigh, or snp 235s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 235s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 235s 235s Paired-end options: 235s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 235s have the same insert length (implies --rm-unpaired-reads) 235s --rm-unpaired-reads: discard unpaired reads 235s --ignore-pe-reads: ignore paired-end reads even if present in the input 235s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 235s 235s Advanced options: 235s (De novo mode) 235s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 235s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 235s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 235s --write-alignments: save read alignments (heavy BAM files) 235s 235s (Reference-based mode) 235s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 235s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 235s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 235s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 235s 235s --details: write a heavier output 235s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 235s iterate over when building the graph of allele cooccurrences for 235s SNP phasing (default: 1,2) 235s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 235s genotypes during phasing 235s 235s kmer_filter 2.68 235s 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] 235s f: path to the input file if processing single-end seqeunces. 235s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 235s p: path to a directory of files (for single-end files only). 235s 1: specify the first in a pair of files to be processed together. 235s 2: specify the second in a pair of files to be processed together. 235s o: path to output the processed files. 235s y: output type, either 'fastq' or 'fasta' (default fastq). 235s D: capture discarded reads to a file. 235s h: display this help message. 235s 235s Filtering options: 235s --rare: turn on filtering based on rare k-mers. 235s --abundant: turn on filtering based on abundant k-mers. 235s --k-len : specify k-mer size (default 15). 235s 235s Advanced filtering options: 235s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 235s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 235s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 235s 235s Normalize data: 235s --normalize : normalize read depth according to k-mer coverage. 235s 235s Characterizing K-mers: 235s --write-k-freq: write kmers along with their frequency of occurrence and exit. 235s --k-dist: print k-mer frequency distribution and exit. 235s 235s Advanced input options: 235s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 235s 235s phasedstacks 2.68 235s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 235s b: Stacks batch ID. 235s P: path to the phased output files. 235s S: path to the Stacks output files. 235s t: input file type. Supported types: fastphase, and beagle. 235s p: number of processes to run in parallel sections of code. 235s M: path to the population map, a tab separated file describing which individuals belong in which population. 235s v: print program version. 235s h: display this help message. 235s --haplotypes: data were phased as RAD locus haplotypes. 235s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 235s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 235s 235s Filtering options: 235s --skip-zeros: do not include D' values of zero in the D' output. 235s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 235s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 235s 235s populations 2.68 235s Usage: 235s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 235s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 235s 235s -P,--in-path: path to a directory containing Stacks output files. 235s -V,--in-vcf: path to a standalone input VCF file. 235s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 235s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 235s -t,--threads: number of threads to run in parallel sections of code. 235s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 235s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 235s 235s Data Filtering: 235s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 235s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 235s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 235s -H,--filter-haplotype-wise: apply the above filters haplotype wise 235s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 235s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 235s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 235s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 235s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 235s 235s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 235s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 235s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 235s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 235s 235s Locus stats: 235s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 235s 235s Fstats: 235s --fstats: enable SNP and haplotype-based F statistics. 235s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 235s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 235s 235s Kernel-smoothing algorithm: 235s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 235s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 235s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 235s (Note: turning on smoothing implies --ordered-export.) 235s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 235s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 235s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 235s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 235s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 235s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 235s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 235s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 235s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 235s 235s File output options: 235s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 235s --fasta-loci: output locus consensus sequences in FASTA format. 235s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 235s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 235s --vcf-all: output all sites in Variant Call Format (VCF). 235s --genepop: output SNPs and haplotypes in GenePop format. 235s --structure: output results in Structure format. 235s --radpainter: output results in fineRADstructure/RADpainter format. 235s --plink: output genotypes in PLINK format. 235s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 235s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 235s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 235s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 235s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 235s --gtf: output locus positions in a GTF annotation file. 235s --no-hap-exports: omit haplotype outputs. 235s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 235s 235s Genetic map output options (population map must specify a genetic cross): 235s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 235s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 235s 235s Additional options: 235s -h,--help: display this help message. 235s -v,--version: print program version. 235s --verbose: turn on additional logging. 235s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 235s process_radtags 2.68 235s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 235s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 235s 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] 235s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 235s 235s -p,--in-path: path to a directory of files. 235s -P,--paired: files contained within the directory are paired. 235s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 235s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 235s -f: path to the input file if processing single-end sequences. 235s -1: first input file in a set of paired-end sequences. 235s -2: second input file in a set of paired-end sequences. 235s -o,--out-path: path to output the processed files. 235s --basename: specify the prefix of the output files when using -f or -1/-2. 235s 235s --threads: number of threads to run. 235s -c,--clean: clean data, remove any read with an uncalled base ('N'). 235s -q,--quality: discard reads with low quality (phred) scores. 235s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 235s -t,--truncate: truncate final read length to this value. 235s -D,--discards: capture discarded reads to a file. 235s 235s Barcode options: 235s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 235s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 235s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 235s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 235s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 235s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 235s --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). 235s 235s Restriction enzyme options: 235s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 235s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 235s Currently supported enzymes include: 235s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 235s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 235s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 235s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 235s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 235s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 235s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 235s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 235s 235s Protocol-specific options: 235s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 235s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 235s 235s Adapter options: 235s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 235s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 235s --adapter-mm : number of mismatches allowed in the adapter sequence. 235s 235s Input/Output options: 235s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 235s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 235s --retain-header: retain unmodified FASTQ headers in the output. 235s --merge: if no barcodes are specified, merge all input files into a single output file. 235s 235s Advanced options: 235s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 235s --disable-rad-check: disable checking if the RAD cut site is intact. 235s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 235s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 235s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 235s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 235s --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). 235s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 235s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 235s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 235s process_shortreads 2.68 235s 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] 235s f: path to the input file if processing single-end seqeunces. 235s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 235s p: path to a directory of single-end Illumina files. 235s 1: first input file in a set of paired-end sequences. 235s 2: second input file in a set of paired-end sequences. 235s P: specify that input is paired (for use with '-p'). 235s I: specify that the paired-end reads are interleaved in single files. 235s o: path to output the processed files. 235s y: output type, either 'fastq' or 'fasta' (default gzfastq). 235s b: a list of barcodes for this run. 235s c: clean data, remove any read with an uncalled base. 235s q: discard reads with low quality scores. 235s r: rescue barcodes. 235s t: truncate final read length to this value. 235s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 235s D: capture discarded reads to a file. 235s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 235s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 235s h: display this help message. 235s 235s Barcode options: 235s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 235s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 235s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 235s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 235s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 235s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 235s --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). 235s 235s Adapter options: 235s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 235s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 235s --adapter-mm : number of mismatches allowed in the adapter sequence. 235s 235s Output options: 235s --retain-header: retain unmodified FASTQ headers in the output. 235s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 235s 235s Advanced options: 235s --no-read-trimming: do not trim low quality reads, just discard them. 235s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 235s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 235s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 235s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 235s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 235s ref_map.pl 2.68 235s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 235s 235s Input/Output files: 235s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 235s --popmap: path to a population map file (format is " TAB ", one sample per line). 235s -s: spacer for file names: by default this is empty and the program looks for files 235s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 235s named 'SAMPLE_NAME.SPACER.bam'. 235s -o,--out-path: path to an output directory. 235s 235s General options: 235s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 235s -T: the number of threads/CPUs to use (default: 1). 235s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 235s that would be executed. 235s 235s SNP model options: 235s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 235s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 235s 235s Paired-end options: 235s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 235s the same insert length. 235s --ignore-pe-reads: ignore paired-end reads even if present in the input 235s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 235s 235s Population filtering options: 235s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 235s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 235s 235s Miscellaneous: 235s --time-components (for benchmarking) 235s sstacks 2.68 235s sstacks -P dir -M popmap [-t n_threads] 235s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 235s -P,--in-path: path to the directory containing Stacks files. 235s -M,--popmap: path to a population map file from which to take sample names. 235s -s,--sample: filename prefix from which to load sample loci. 235s -c,--catalog: path to the catalog. 235s -t,--threads: enable parallel execution with n_threads threads. 235s -o,--out-path: output path to write results. 235s -x: don't verify haplotype of matching locus. 235s 235s Gapped assembly options: 235s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 235s usage: 235s stacks-dist-extract logfile [section] 235s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 235s cat logfile | stacks-dist-extract [--pretty] [--section section] 235s 235s Export a paricular section of a Stacks log or distribs file. If you supply a 235s log path alone, stacks-dist-extract will print the available sections to 235s output. The log file can also be supplied via stdin. 235s 235s options: 235s -h, --help show this help message and exit 235s -p, --pretty Output data as a table with columns lined up. 235s -o, --out-path path Path to output file. 235s -s, --section section 235s Name of section to output from the log file. 235s Usage: 235s stacks-gdb PROGRAM ARGUMENTS 235s 235s e.g. 235s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 235s 235s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 235s case of a crash it will print additional information, helping us in fixing the 235s crash. 235s 235s This utility requires GDB, the GNU Debugger, to be installed on the system where 235s Stacks is run. You can check whether this is the case by just typing: 235s 235s gdb --version 235s 235s at the command prompt. Note that you may need to load the corresponding module. 235s GDB is standard scientific software, but may not be installed on some systems. 235s For further information please contact the administrators of your system; 235s trying to install GDB without administrator priviledges is not recommended. 235s 235s For questions please contact us, e.g. at stacks-users@googlegroups.com 235s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 235s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 235s [--version] 235s 235s Extracts the coordinates of the RAD loci from the given BAM file into a 235s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 235s 'catalog.calls' files so that they include the genomic coordinates given in 235s the input BAM file. 235s 235s options: 235s -h, --help show this help message and exit 235s -P, --in-path path Path to a directory containing Stacks ouput files. 235s -B, --bam-path path Path to a SAM or BAM file containing alignment of de 235s novo catalog loci to a reference genome. 235s -O, --out-path path Path to write the integrated ouput files. 235s -q, --min_mapq MIN_MAPQ 235s Minimum mapping quality as listed in the BAM file 235s (default 20). 235s -a, --min_alncov MIN_ALNCOV 235s Minimum fraction of the de novo catalog locus that 235s must participate in the alignment (default 0.6). 235s -p, --min_pctid MIN_PCTID 235s Minimum BLAST-style percent identity of the largest 235s alignment fragment for a de novo catalog locus 235s (default 0.6). 235s --verbose Provide verbose output. 235s --version show program's version number and exit 235s usage: 235s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 235s 235s Displays the read alignments of the given sample for the given locus, in text 235s format, to the standard output. Requires gstacks to have been run with the 235s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 235s tsv2bam 2.68 235s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 235s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 235s 235s -P,--in-dir: input directory. 235s -M,--popmap: population map. 235s -s,--sample: name of one sample. 235s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 235s -t: number of threads to use (default: 1). 235s 235s ustacks 2.68 235s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 235s -f,--file: input file path. 235s -o,--out-path: output path to write results. 235s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 235s -m: Minimum number of reads to seed a new stack (default 3). 235s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 235s -t,--threads: enable parallel execution with num_threads threads. 235s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 235s -n,--name: a name for the sample (default: input file name minus the suffix). 235s -R: retain unused reads. 235s -H: disable calling haplotypes from secondary reads. 235s 235s Stack assembly options: 235s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 235s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 235s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 235s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 235s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 235s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 235s 235s Gapped assembly options: 235s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 235s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 235s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 235s 235s Model options: 235s --model-type: either 'snp' (default), 'bounded', or 'fixed' 235s For the SNP or Bounded SNP model: 235s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 235s For the Bounded SNP model: 235s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 235s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 235s For the Fixed model: 235s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 235s 235s h: display this help message. 235s autopkgtest [17:00:36]: test run-unit-test: -----------------------] 236s autopkgtest [17:00:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 236s run-unit-test PASS (superficial) 236s autopkgtest [17:00:37]: @@@@@@@@@@@@@@@@@@@@ summary 236s run-unit-test PASS (superficial) 242s nova [W] Using flock in prodstack6-arm64 242s Creating nova instance adt-plucky-arm64-stacks-20250315-165641-juju-7f2275-prod-proposed-migration-environment-20-25e36112-84c7-40ba-a6e4-2307be00e4b9 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 242s nova [W] Timed out waiting for fbfe9298-dd35-435d-a01f-76a47ab50631 to get deleted.