0s autopkgtest [13:10:31]: starting date and time: 2025-02-16 13:10:31+0000 0s autopkgtest [13:10:31]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:10:31]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ofogvonw/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-1.secgroup --name adt-plucky-arm64-stacks-20250216-131031-juju-7f2275-prod-proposed-migration-environment-15-8d8cc267-edc9-48a3-a8b4-8110b6f65b6c --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 227s autopkgtest [13:14:18]: testbed dpkg architecture: arm64 227s autopkgtest [13:14:18]: testbed apt version: 2.9.28 228s autopkgtest [13:14:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 228s autopkgtest [13:14:19]: testbed release detected to be: None 229s autopkgtest [13:14:20]: updating testbed package index (apt update) 229s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 230s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 230s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 230s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 230s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [72.9 kB] 230s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 230s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [789 kB] 230s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 230s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [93.2 kB] 230s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 230s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [982 kB] 230s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.0 kB] 230s Fetched 2082 kB in 1s (1998 kB/s) 231s Reading package lists... 232s + lsb_release --codename --short 232s + RELEASE=plucky 232s + cat 232s + [ plucky != trusty ] 232s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 232s Reading package lists... 233s Building dependency tree... 233s Reading state information... 234s Calculating upgrade... 235s The following packages will be upgraded: 235s pci.ids 235s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 235s Need to get 284 kB of archives. 235s After this operation, 1024 B of additional disk space will be used. 235s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pci.ids all 0.0~2025.02.12-1 [284 kB] 236s Fetched 284 kB in 0s (690 kB/s) 236s (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 ... 116609 files and directories currently installed.) 236s Preparing to unpack .../pci.ids_0.0~2025.02.12-1_all.deb ... 236s Unpacking pci.ids (0.0~2025.02.12-1) over (0.0~2025.02.05-1) ... 236s Setting up pci.ids (0.0~2025.02.12-1) ... 237s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 237s + /usr/lib/apt/apt-helper analyze-pattern ?true 237s + uname -r 237s + sed s/\./\\./g 237s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 237s + apt list ?obsolete 237s + tail -n+2 237s + cut -d/ -f1 237s + grep -v ^linux-.*6\.12\.0-15-generic.* 237s + true 237s + obsolete_pkgs= 237s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 237s Reading package lists... 237s Building dependency tree... 237s Reading state information... 238s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 238s + grep -q trusty /etc/lsb-release 238s + [ ! -d /usr/share/doc/unattended-upgrades ] 238s + [ ! -d /usr/share/doc/lxd ] 238s + [ ! -d /usr/share/doc/lxd-client ] 238s + [ ! -d /usr/share/doc/snapd ] 238s + type iptables 238s + cat 238s + chmod 755 /etc/rc.local 238s + . /etc/rc.local 238s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 238s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 238s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 238s + uname -m 238s + [ aarch64 = ppc64le ] 238s + [ -d /run/systemd/system ] 238s + systemd-detect-virt --quiet --vm 238s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 238s + cat 238s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 238s + echo COMPRESS=lz4 238s autopkgtest [13:14:29]: upgrading testbed (apt dist-upgrade and autopurge) 238s Reading package lists... 239s Building dependency tree... 239s Reading state information... 239s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 240s Entering ResolveByKeep 241s 241s The following packages will be upgraded: 241s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 241s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 241s Need to get 10.7 MB of archives. 241s After this operation, 358 kB of additional disk space will be used. 241s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu1 [24.0 kB] 242s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu1 [1750 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu1 [4246 kB] 242s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu1 [2910 kB] 242s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu1 [600 kB] 242s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 243s Preconfiguring packages ... 243s Fetched 10.7 MB in 1s (11.1 MB/s) 243s (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 ... 116609 files and directories currently installed.) 243s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_arm64.deb ... 243s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 243s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_arm64.deb ... 243s Unpacking libc6-dev:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 243s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 243s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 243s Preparing to unpack .../libc6_2.41-1ubuntu1_arm64.deb ... 243s Checking for services that may need to be restarted... 243s Checking init scripts... 243s Checking for services that may need to be restarted... 243s Checking init scripts... 244s Stopping some services possibly affected by the upgrade (will be restarted later): 244s cron: stopping...done. 244s 244s Unpacking libc6:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 244s Setting up libc6:arm64 (2.41-1ubuntu1) ... 244s Checking for services that may need to be restarted... 244s Checking init scripts... 244s Restarting services possibly affected by the upgrade: 244s cron: restarting...done. 244s 244s Services restarted successfully. 244s (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 ... 116610 files and directories currently installed.) 244s Preparing to unpack .../libc-bin_2.41-1ubuntu1_arm64.deb ... 244s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 244s Setting up libc-bin (2.41-1ubuntu1) ... 245s (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 ... 116610 files and directories currently installed.) 245s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_arm64.deb ... 245s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 245s Setting up iproute2 (6.13.0-1ubuntu1) ... 245s Setting up locales (2.41-1ubuntu1) ... 245s Installing new version of config file /etc/locale.alias ... 246s Generating locales (this might take a while)... 248s en_US.UTF-8... done 248s Generation complete. 248s Setting up libc-dev-bin (2.41-1ubuntu1) ... 248s Setting up libc6-dev:arm64 (2.41-1ubuntu1) ... 248s Processing triggers for man-db (2.13.0-1) ... 250s Processing triggers for systemd (257.2-3ubuntu1) ... 251s Reading package lists... 251s Building dependency tree... 251s Reading state information... 252s Starting pkgProblemResolver with broken count: 0 252s Starting 2 pkgProblemResolver with broken count: 0 252s Done 253s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 256s autopkgtest [13:14:47]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 256s autopkgtest [13:14:47]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 258s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (dsc) [2070 B] 258s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (tar) [371 kB] 258s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (diff) [12.2 kB] 258s gpgv: Signature made Sat Aug 31 10:00:49 2024 UTC 258s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 258s gpgv: issuer "emollier@debian.org" 258s gpgv: Can't check signature: No public key 258s dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-1.dsc: no acceptable signature found 258s autopkgtest [13:14:49]: testing package stacks version 2.68+dfsg-1 258s autopkgtest [13:14:49]: build not needed 259s autopkgtest [13:14:50]: test run-unit-test: preparing testbed 259s Reading package lists... 260s Building dependency tree... 260s Reading state information... 260s Starting pkgProblemResolver with broken count: 0 260s Starting 2 pkgProblemResolver with broken count: 0 260s Done 261s The following NEW packages will be installed: 261s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 261s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 261s Need to get 3191 kB of archives. 261s After this operation, 10.1 MB of additional disk space will be used. 261s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libdbi-perl arm64 1.647-1 [827 kB] 262s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 262s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-17ubuntu1 [145 kB] 262s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 262s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 262s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB] 262s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 stacks arm64 2.68+dfsg-1 [1040 kB] 262s Fetched 3191 kB in 1s (4416 kB/s) 262s Selecting previously unselected package libdbi-perl:arm64. 262s (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 ... 116611 files and directories currently installed.) 262s Preparing to unpack .../0-libdbi-perl_1.647-1_arm64.deb ... 262s Unpacking libdbi-perl:arm64 (1.647-1) ... 262s Selecting previously unselected package libdeflate0:arm64. 262s Preparing to unpack .../1-libdeflate0_1.23-1_arm64.deb ... 262s Unpacking libdeflate0:arm64 (1.23-1) ... 262s Selecting previously unselected package libgomp1:arm64. 262s Preparing to unpack .../2-libgomp1_14.2.0-17ubuntu1_arm64.deb ... 262s Unpacking libgomp1:arm64 (14.2.0-17ubuntu1) ... 262s Selecting previously unselected package libhtscodecs2:arm64. 262s Preparing to unpack .../3-libhtscodecs2_1.6.1-1_arm64.deb ... 262s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 262s Selecting previously unselected package libhts3t64:arm64. 262s Preparing to unpack .../4-libhts3t64_1.21+ds-1_arm64.deb ... 262s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 262s Selecting previously unselected package samtools. 262s Preparing to unpack .../5-samtools_1.21-1_arm64.deb ... 262s Unpacking samtools (1.21-1) ... 262s Selecting previously unselected package stacks. 262s Preparing to unpack .../6-stacks_2.68+dfsg-1_arm64.deb ... 262s Unpacking stacks (2.68+dfsg-1) ... 263s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 263s Setting up libdeflate0:arm64 (1.23-1) ... 263s Setting up libgomp1:arm64 (14.2.0-17ubuntu1) ... 263s Setting up libhts3t64:arm64 (1.21+ds-1) ... 263s Setting up libdbi-perl:arm64 (1.647-1) ... 263s Setting up samtools (1.21-1) ... 263s Setting up stacks (2.68+dfsg-1) ... 263s Processing triggers for man-db (2.13.0-1) ... 263s Processing triggers for libc-bin (2.41-1ubuntu1) ... 264s autopkgtest [13:14:55]: test run-unit-test: [----------------------- 264s Stacks - a pipeline for building loci from short-read sequences 264s v2.68+dfsg http://creskolab.uoregon.edu/stacks/ 264s 264s This is the Stacks wrapper script for Debian. Usage: 264s stacks 264s 264s Programs available are: 264s clone_filter ref_map 264s cstacks sstacks 264s denovo_map stacks-dist-extract 264s gstacks stacks-gdb 264s kmer_filter stacks-integrate-alignments 264s phasedstacks stacks-private-alleles 264s populations stacks-samtools-tview 264s process_radtags tsv2bam 264s process_shortreads ustacks 264s 264s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 264s 264s clone_filter 2.68 264s 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] 264s f: path to the input file if processing single-end sequences. 264s p: path to a directory of files. 264s P: files contained within directory specified by '-p' are paired. 264s 1: first input file in a set of paired-end sequences. 264s 2: second input file in a set of paired-end sequences. 264s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 264s o: path to output the processed files. 264s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 264s D: capture discarded reads to a file. 264s h: display this help message. 264s --oligo-len-1 len: length of the single-end oligo sequence in data set. 264s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 264s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 264s 264s Oligo sequence options: 264s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 264s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 264s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 264s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 264s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 264s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 264s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 264s --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). 264s 264s cstacks 2.68 264s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 264s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 264s 264s -P,--in-path: path to the directory containing Stacks files. 264s -M,--popmap: path to a population map file. 264s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 264s -t,--threads: enable parallel execution with num_threads threads. 264s -s: sample prefix from which to load loci into the catalog. 264s -o,--outpath: output path to write results. 264s -c,--catalog : add to an existing catalog. 264s 264s Gapped assembly options: 264s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 264s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 264s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 264s 264s Advanced options: 264s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 264s --report-mmatches: report query loci that match more than one catalog locus. 264s denovo_map.pl 2.68 264s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 264s 264s Input/Output files: 264s --samples: path to the directory containing the reads files for each sample. 264s --popmap: path to a population map file (format is " TAB ", one sample per line). 264s -o,--out-path: path to an output directory. 264s 264s General options: 264s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 264s -T, --threads: the number of threads/CPUs to use (default: 1). 264s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 264s --resume: resume executing the pipeline from a previous run. 264s 264s Stack assembly options: 264s -M: number of mismatches allowed between stacks within individuals (for ustacks). 264s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 264s 264s SNP model options: 264s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 264s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 264s 264s Paired-end options: 264s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 264s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 264s the same insert length. 264s 264s Population filtering options: 264s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 264s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 264s 264s For large datasets: 264s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 264s 264s Miscellaneous: 264s --time-components (for benchmarking) 264s gstacks 2.68 264s 264s De novo mode: 264s gstacks -P stacks_dir -M popmap 264s 264s -P: input directory containing '*.matches.bam' files created by the 264s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 264s 264s Reference-based mode: 264s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 264s gstacks -B bam_file [-B ...] -O out_dir 264s 264s -I: input directory containing BAM files 264s -S: with -I/-M, suffix to use to build BAM file names: by default this 264s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 264s -B: input BAM file(s) 264s 264s The input BAM file(s) must be sorted by coordinate. 264s With -B, records must be assigned to samples using BAM "reads groups" 264s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 264s must be consistent if repeated different files. Note that with -I, read 264s groups are unneeded and ignored. 264s 264s For both modes: 264s -M: path to a population map giving the list of samples 264s -O: output directory (default: none with -B; with -P same as the input 264s directory) 264s -t,--threads: number of threads to use (default: 1) 264s 264s SNP Model options: 264s --model: model to use to call variants and genotypes; one of 264s marukilow (default), marukihigh, or snp 264s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 264s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 264s 264s Paired-end options: 264s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 264s have the same insert length (implies --rm-unpaired-reads) 264s --rm-unpaired-reads: discard unpaired reads 264s --ignore-pe-reads: ignore paired-end reads even if present in the input 264s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 264s 264s Advanced options: 264s (De novo mode) 264s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 264s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 264s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 264s --write-alignments: save read alignments (heavy BAM files) 264s 264s (Reference-based mode) 264s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 264s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 264s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 264s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 264s 264s --details: write a heavier output 264s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 264s iterate over when building the graph of allele cooccurrences for 264s SNP phasing (default: 1,2) 264s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 264s genotypes during phasing 264s 264s kmer_filter 2.68 264s 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] 264s f: path to the input file if processing single-end seqeunces. 264s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 264s p: path to a directory of files (for single-end files only). 264s 1: specify the first in a pair of files to be processed together. 264s 2: specify the second in a pair of files to be processed together. 264s o: path to output the processed files. 264s y: output type, either 'fastq' or 'fasta' (default fastq). 264s D: capture discarded reads to a file. 264s h: display this help message. 264s 264s Filtering options: 264s --rare: turn on filtering based on rare k-mers. 264s --abundant: turn on filtering based on abundant k-mers. 264s --k-len : specify k-mer size (default 15). 264s 264s Advanced filtering options: 264s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 264s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 264s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 264s 264s Normalize data: 264s --normalize : normalize read depth according to k-mer coverage. 264s 264s Characterizing K-mers: 264s --write-k-freq: write kmers along with their frequency of occurrence and exit. 264s --k-dist: print k-mer frequency distribution and exit. 264s 264s Advanced input options: 264s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 264s 264s phasedstacks 2.68 264s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 264s b: Stacks batch ID. 264s P: path to the phased output files. 264s S: path to the Stacks output files. 264s t: input file type. Supported types: fastphase, and beagle. 264s p: number of processes to run in parallel sections of code. 264s M: path to the population map, a tab separated file describing which individuals belong in which population. 264s v: print program version. 264s h: display this help message. 264s --haplotypes: data were phased as RAD locus haplotypes. 264s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 264s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 264s 264s Filtering options: 264s --skip-zeros: do not include D' values of zero in the D' output. 264s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 264s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 264s 264s populations 2.68 264s Usage: 264s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 264s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 264s 264s -P,--in-path: path to a directory containing Stacks output files. 264s -V,--in-vcf: path to a standalone input VCF file. 264s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 264s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 264s -t,--threads: number of threads to run in parallel sections of code. 264s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 264s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 264s 264s Data Filtering: 264s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 264s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 264s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 264s -H,--filter-haplotype-wise: apply the above filters haplotype wise 264s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 264s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 264s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 264s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 264s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 264s 264s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 264s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 264s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 264s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 264s 264s Locus stats: 264s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 264s 264s Fstats: 264s --fstats: enable SNP and haplotype-based F statistics. 264s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 264s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 264s 264s Kernel-smoothing algorithm: 264s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 264s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 264s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 264s (Note: turning on smoothing implies --ordered-export.) 264s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 264s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 264s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 264s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 264s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 264s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 264s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 264s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 264s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 264s 264s File output options: 264s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 264s --fasta-loci: output locus consensus sequences in FASTA format. 264s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 264s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 264s --vcf-all: output all sites in Variant Call Format (VCF). 264s --genepop: output SNPs and haplotypes in GenePop format. 264s --structure: output results in Structure format. 264s --radpainter: output results in fineRADstructure/RADpainter format. 264s --plink: output genotypes in PLINK format. 264s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 264s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 264s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 264s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 264s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 264s --gtf: output locus positions in a GTF annotation file. 264s --no-hap-exports: omit haplotype outputs. 264s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 264s 264s Genetic map output options (population map must specify a genetic cross): 264s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 264s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 264s 264s Additional options: 264s -h,--help: display this help message. 264s -v,--version: print program version. 264s --verbose: turn on additional logging. 264s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 264s process_radtags 2.68 264s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 264s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 264s 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] 264s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 264s 264s -p,--in-path: path to a directory of files. 264s -P,--paired: files contained within the directory are paired. 264s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 264s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 264s -f: path to the input file if processing single-end sequences. 264s -1: first input file in a set of paired-end sequences. 264s -2: second input file in a set of paired-end sequences. 264s -o,--out-path: path to output the processed files. 264s --basename: specify the prefix of the output files when using -f or -1/-2. 264s 264s --threads: number of threads to run. 264s -c,--clean: clean data, remove any read with an uncalled base ('N'). 264s -q,--quality: discard reads with low quality (phred) scores. 264s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 264s -t,--truncate: truncate final read length to this value. 264s -D,--discards: capture discarded reads to a file. 264s 264s Barcode options: 264s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 264s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 264s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 264s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 264s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 264s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 264s --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). 264s 264s Restriction enzyme options: 264s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 264s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 264s Currently supported enzymes include: 264s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 264s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 264s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 264s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 264s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 264s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 264s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 264s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 264s 264s Protocol-specific options: 264s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 264s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 264s 264s Adapter options: 264s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 264s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 264s --adapter-mm : number of mismatches allowed in the adapter sequence. 264s 264s Input/Output options: 264s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 264s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 264s --retain-header: retain unmodified FASTQ headers in the output. 264s --merge: if no barcodes are specified, merge all input files into a single output file. 264s 264s Advanced options: 264s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 264s --disable-rad-check: disable checking if the RAD cut site is intact. 264s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 264s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 264s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 264s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 264s --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). 264s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 264s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 264s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 264s process_shortreads 2.68 264s 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] 264s f: path to the input file if processing single-end seqeunces. 264s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 264s p: path to a directory of single-end Illumina files. 264s 1: first input file in a set of paired-end sequences. 264s 2: second input file in a set of paired-end sequences. 264s P: specify that input is paired (for use with '-p'). 264s I: specify that the paired-end reads are interleaved in single files. 264s o: path to output the processed files. 264s y: output type, either 'fastq' or 'fasta' (default gzfastq). 264s b: a list of barcodes for this run. 264s c: clean data, remove any read with an uncalled base. 264s q: discard reads with low quality scores. 264s r: rescue barcodes. 264s t: truncate final read length to this value. 264s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 264s D: capture discarded reads to a file. 264s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 264s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 264s h: display this help message. 264s 264s Barcode options: 264s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 264s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 264s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 264s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 264s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 264s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 264s --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). 264s 264s Adapter options: 264s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 264s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 264s --adapter-mm : number of mismatches allowed in the adapter sequence. 264s 264s Output options: 264s --retain-header: retain unmodified FASTQ headers in the output. 264s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 264s 264s Advanced options: 264s --no-read-trimming: do not trim low quality reads, just discard them. 264s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 264s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 264s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 264s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 264s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 264s ref_map.pl 2.68 264s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 264s 264s Input/Output files: 264s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 264s --popmap: path to a population map file (format is " TAB ", one sample per line). 264s -s: spacer for file names: by default this is empty and the program looks for files 264s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 264s named 'SAMPLE_NAME.SPACER.bam'. 264s -o,--out-path: path to an output directory. 264s 264s General options: 264s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 264s -T: the number of threads/CPUs to use (default: 1). 264s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 264s that would be executed. 264s 264s SNP model options: 264s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 264s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 264s 264s Paired-end options: 264s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 264s the same insert length. 264s --ignore-pe-reads: ignore paired-end reads even if present in the input 264s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 264s 264s Population filtering options: 264s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 264s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 264s 264s Miscellaneous: 264s --time-components (for benchmarking) 264s sstacks 2.68 264s sstacks -P dir -M popmap [-t n_threads] 264s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 264s -P,--in-path: path to the directory containing Stacks files. 264s -M,--popmap: path to a population map file from which to take sample names. 264s -s,--sample: filename prefix from which to load sample loci. 264s -c,--catalog: path to the catalog. 264s -t,--threads: enable parallel execution with n_threads threads. 264s -o,--out-path: output path to write results. 264s -x: don't verify haplotype of matching locus. 264s 264s Gapped assembly options: 264s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 264s usage: 264s stacks-dist-extract logfile [section] 264s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 264s cat logfile | stacks-dist-extract [--pretty] [--section section] 264s 264s Export a paricular section of a Stacks log or distribs file. If you supply a 264s log path alone, stacks-dist-extract will print the available sections to 264s output. The log file can also be supplied via stdin. 264s 264s options: 264s -h, --help show this help message and exit 264s -p, --pretty Output data as a table with columns lined up. 264s -o, --out-path path Path to output file. 264s -s, --section section 264s Name of section to output from the log file. 264s Usage: 264s stacks-gdb PROGRAM ARGUMENTS 264s 264s e.g. 264s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 264s 264s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 264s case of a crash it will print additional information, helping us in fixing the 264s crash. 264s 264s This utility requires GDB, the GNU Debugger, to be installed on the system where 264s Stacks is run. You can check whether this is the case by just typing: 264s 264s gdb --version 264s 264s at the command prompt. Note that you may need to load the corresponding module. 264s GDB is standard scientific software, but may not be installed on some systems. 264s For further information please contact the administrators of your system; 264s trying to install GDB without administrator priviledges is not recommended. 264s 264s For questions please contact us, e.g. at stacks-users@googlegroups.com 264s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 264s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 264s [--version] 264s 264s Extracts the coordinates of the RAD loci from the given BAM file into a 264s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 264s 'catalog.calls' files so that they include the genomic coordinates given in 264s the input BAM file. 264s 264s options: 264s -h, --help show this help message and exit 264s -P, --in-path path Path to a directory containing Stacks ouput files. 264s -B, --bam-path path Path to a SAM or BAM file containing alignment of de 264s novo catalog loci to a reference genome. 264s -O, --out-path path Path to write the integrated ouput files. 264s -q, --min_mapq MIN_MAPQ 264s Minimum mapping quality as listed in the BAM file 264s (default 20). 264s -a, --min_alncov MIN_ALNCOV 264s Minimum fraction of the de novo catalog locus that 264s must participate in the alignment (default 0.6). 264s -p, --min_pctid MIN_PCTID 264s Minimum BLAST-style percent identity of the largest 264s alignment fragment for a de novo catalog locus 264s (default 0.6). 264s --verbose Provide verbose output. 264s --version show program's version number and exit 264s usage: 264s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 264s 264s Displays the read alignments of the given sample for the given locus, in text 264s format, to the standard output. Requires gstacks to have been run with the 264s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 264s tsv2bam 2.68 264s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 264s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 264s 264s -P,--in-dir: input directory. 264s -M,--popmap: population map. 264s -s,--sample: name of one sample. 264s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 264s -t: number of threads to use (default: 1). 264s 264s ustacks 2.68 264s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 264s -f,--file: input file path. 264s -o,--out-path: output path to write results. 264s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 264s -m: Minimum number of reads to seed a new stack (default 3). 264s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 264s -t,--threads: enable parallel execution with num_threads threads. 264s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 264s -n,--name: a name for the sample (default: input file name minus the suffix). 264s -R: retain unused reads. 264s -H: disable calling haplotypes from secondary reads. 264s 264s Stack assembly options: 264s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 264s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 264s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 264s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 264s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 264s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 264s 264s Gapped assembly options: 264s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 264s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 264s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 264s 264s Model options: 264s --model-type: either 'snp' (default), 'bounded', or 'fixed' 264s For the SNP or Bounded SNP model: 264s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 264s For the Bounded SNP model: 264s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 264s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 264s For the Fixed model: 264s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 264s 264s h: display this help message. 265s autopkgtest [13:14:56]: test run-unit-test: -----------------------] 265s run-unit-test PASS (superficial) 265s autopkgtest [13:14:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 265s autopkgtest [13:14:56]: @@@@@@@@@@@@@@@@@@@@ summary 265s run-unit-test PASS (superficial) 356s nova [W] Using flock in prodstack6-arm64 356s Creating nova instance adt-plucky-arm64-stacks-20250216-131031-juju-7f2275-prod-proposed-migration-environment-15-8d8cc267-edc9-48a3-a8b4-8110b6f65b6c from image adt/ubuntu-plucky-arm64-server-20250216.img (UUID a098a761-c895-418e-827f-00d410a1ece9)... 356s nova [W] Timed out waiting for ff40a73e-55a7-4a8c-ba66-d76c07471088 to get deleted.