0s autopkgtest [23:01:07]: starting date and time: 2025-02-15 23:01:07+0000 0s autopkgtest [23:01:07]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:01:07]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ade8b4qz/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-13.secgroup --name adt-plucky-amd64-stacks-20250215-230106-juju-7f2275-prod-proposed-migration-environment-20-12949107-b6e5-422c-b45b-b1f3e38adf76 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 64s autopkgtest [23:02:11]: testbed dpkg architecture: amd64 65s autopkgtest [23:02:12]: testbed apt version: 2.9.28 65s autopkgtest [23:02:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s autopkgtest [23:02:12]: testbed release detected to be: None 66s autopkgtest [23:02:13]: updating testbed package index (apt update) 66s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 66s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 67s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.3 kB] 67s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 67s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 67s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [828 kB] 67s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [175 kB] 67s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [154 kB] 67s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 67s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 67s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [403 kB] 67s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [949 kB] 67s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 67s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB] 67s Fetched 2734 kB in 1s (2660 kB/s) 68s Reading package lists... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade... 69s The following packages will be upgraded: 69s libtasn1-6 69s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 51.2 kB of archives. 69s After this operation, 22.5 kB of additional disk space will be used. 69s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 70s Fetched 51.2 kB in 0s (182 kB/s) 70s (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 ... 108914 files and directories currently installed.) 70s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 70s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 70s Setting up libtasn1-6:amd64 (4.20.0-2) ... 70s Processing triggers for libc-bin (2.40-4ubuntu1) ... 70s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 71s autopkgtest [23:02:18]: upgrading testbed (apt dist-upgrade and autopurge) 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 72s Starting 2 pkgProblemResolver with broken count: 0 72s Done 72s Entering ResolveByKeep 72s 72s The following packages will be upgraded: 72s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 72s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 11.8 MB of archives. 72s After this operation, 746 kB of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 73s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 73s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 73s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 74s Preconfiguring packages ... 74s Fetched 11.8 MB in 1s (11.6 MB/s) 74s (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 ... 108914 files and directories currently installed.) 74s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 74s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 74s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 74s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 74s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 74s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 74s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 74s Checking for services that may need to be restarted... 74s Checking init scripts... 74s Checking for services that may need to be restarted... 74s Checking init scripts... 75s Stopping some services possibly affected by the upgrade (will be restarted later): 75s cron: stopping...done. 75s 75s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 75s Setting up libc6:amd64 (2.41-1ubuntu1) ... 75s Checking for services that may need to be restarted... 75s Checking init scripts... 75s Restarting services possibly affected by the upgrade: 75s cron: restarting...done. 75s 75s Services restarted successfully. 75s (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 ... 108915 files and directories currently installed.) 75s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 75s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 75s Setting up libc-bin (2.41-1ubuntu1) ... 75s (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 ... 108915 files and directories currently installed.) 75s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 75s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 75s Setting up iproute2 (6.13.0-1ubuntu1) ... 76s Setting up locales (2.41-1ubuntu1) ... 76s Installing new version of config file /etc/locale.alias ... 76s Generating locales (this might take a while)... 78s en_US.UTF-8... done 78s Generation complete. 78s Setting up libc-dev-bin (2.41-1ubuntu1) ... 78s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 78s Processing triggers for man-db (2.13.0-1) ... 79s Processing triggers for systemd (257.2-3ubuntu1) ... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Starting pkgProblemResolver with broken count: 0 80s Starting 2 pkgProblemResolver with broken count: 0 80s Done 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [23:02:30]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 84s autopkgtest [23:02:31]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (dsc) [2070 B] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (tar) [371 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-1 (diff) [12.2 kB] 85s gpgv: Signature made Sat Aug 31 10:00:49 2024 UTC 85s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 85s gpgv: issuer "emollier@debian.org" 85s gpgv: Can't check signature: No public key 85s dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-1.dsc: no acceptable signature found 86s autopkgtest [23:02:33]: testing package stacks version 2.68+dfsg-1 86s autopkgtest [23:02:33]: build not needed 86s autopkgtest [23:02:33]: test run-unit-test: preparing testbed 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 88s The following NEW packages will be installed: 88s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 88s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 3534 kB of archives. 88s After this operation, 10.3 MB of additional disk space will be used. 88s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libdbi-perl amd64 1.647-1 [832 kB] 88s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 88s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-17ubuntu1 [148 kB] 88s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 88s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 88s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB] 88s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 stacks amd64 2.68+dfsg-1 [1189 kB] 89s Fetched 3534 kB in 1s (5075 kB/s) 89s Selecting previously unselected package libdbi-perl:amd64. 89s (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 ... 108916 files and directories currently installed.) 89s Preparing to unpack .../0-libdbi-perl_1.647-1_amd64.deb ... 89s Unpacking libdbi-perl:amd64 (1.647-1) ... 89s Selecting previously unselected package libdeflate0:amd64. 89s Preparing to unpack .../1-libdeflate0_1.23-1_amd64.deb ... 89s Unpacking libdeflate0:amd64 (1.23-1) ... 89s Selecting previously unselected package libgomp1:amd64. 89s Preparing to unpack .../2-libgomp1_14.2.0-17ubuntu1_amd64.deb ... 89s Unpacking libgomp1:amd64 (14.2.0-17ubuntu1) ... 89s Selecting previously unselected package libhtscodecs2:amd64. 89s Preparing to unpack .../3-libhtscodecs2_1.6.1-1_amd64.deb ... 89s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 89s Selecting previously unselected package libhts3t64:amd64. 89s Preparing to unpack .../4-libhts3t64_1.21+ds-1_amd64.deb ... 89s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 89s Selecting previously unselected package samtools. 89s Preparing to unpack .../5-samtools_1.21-1_amd64.deb ... 89s Unpacking samtools (1.21-1) ... 89s Selecting previously unselected package stacks. 89s Preparing to unpack .../6-stacks_2.68+dfsg-1_amd64.deb ... 89s Unpacking stacks (2.68+dfsg-1) ... 89s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 89s Setting up libdeflate0:amd64 (1.23-1) ... 89s Setting up libgomp1:amd64 (14.2.0-17ubuntu1) ... 89s Setting up libhts3t64:amd64 (1.21+ds-1) ... 89s Setting up libdbi-perl:amd64 (1.647-1) ... 89s Setting up samtools (1.21-1) ... 89s Setting up stacks (2.68+dfsg-1) ... 89s Processing triggers for man-db (2.13.0-1) ... 89s Processing triggers for libc-bin (2.41-1ubuntu1) ... 90s autopkgtest [23:02:37]: test run-unit-test: [----------------------- 91s Stacks - a pipeline for building loci from short-read sequences 91s v2.68+dfsg http://creskolab.uoregon.edu/stacks/ 91s 91s This is the Stacks wrapper script for Debian. Usage: 91s stacks 91s 91s Programs available are: 91s clone_filter ref_map 91s cstacks sstacks 91s denovo_map stacks-dist-extract 91s gstacks stacks-gdb 91s kmer_filter stacks-integrate-alignments 91s phasedstacks stacks-private-alleles 91s populations stacks-samtools-tview 91s process_radtags tsv2bam 91s process_shortreads ustacks 91s 91s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 91s 91s clone_filter 2.68 91s 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] 91s f: path to the input file if processing single-end sequences. 91s p: path to a directory of files. 91s P: files contained within directory specified by '-p' are paired. 91s 1: first input file in a set of paired-end sequences. 91s 2: second input file in a set of paired-end sequences. 91s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 91s o: path to output the processed files. 91s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 91s D: capture discarded reads to a file. 91s h: display this help message. 91s --oligo-len-1 len: length of the single-end oligo sequence in data set. 91s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 91s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 91s 91s Oligo sequence options: 91s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 91s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 91s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 91s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 91s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 91s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 91s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 91s --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). 91s 91s cstacks 2.68 91s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 91s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 91s 91s -P,--in-path: path to the directory containing Stacks files. 91s -M,--popmap: path to a population map file. 91s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 91s -t,--threads: enable parallel execution with num_threads threads. 91s -s: sample prefix from which to load loci into the catalog. 91s -o,--outpath: output path to write results. 91s -c,--catalog : add to an existing catalog. 91s 91s Gapped assembly options: 91s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 91s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 91s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 91s 91s Advanced options: 91s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 91s --report-mmatches: report query loci that match more than one catalog locus. 91s denovo_map.pl 2.68 91s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 91s 91s Input/Output files: 91s --samples: path to the directory containing the reads files for each sample. 91s --popmap: path to a population map file (format is " TAB ", one sample per line). 91s -o,--out-path: path to an output directory. 91s 91s General options: 91s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 91s -T, --threads: the number of threads/CPUs to use (default: 1). 91s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 91s --resume: resume executing the pipeline from a previous run. 91s 91s Stack assembly options: 91s -M: number of mismatches allowed between stacks within individuals (for ustacks). 91s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 91s 91s SNP model options: 91s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 91s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 91s 91s Paired-end options: 91s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 91s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 91s the same insert length. 91s 91s Population filtering options: 91s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 91s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 91s 91s For large datasets: 91s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 91s 91s Miscellaneous: 91s --time-components (for benchmarking) 91s gstacks 2.68 91s 91s De novo mode: 91s gstacks -P stacks_dir -M popmap 91s 91s -P: input directory containing '*.matches.bam' files created by the 91s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 91s 91s Reference-based mode: 91s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 91s gstacks -B bam_file [-B ...] -O out_dir 91s 91s -I: input directory containing BAM files 91s -S: with -I/-M, suffix to use to build BAM file names: by default this 91s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 91s -B: input BAM file(s) 91s 91s The input BAM file(s) must be sorted by coordinate. 91s With -B, records must be assigned to samples using BAM "reads groups" 91s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 91s must be consistent if repeated different files. Note that with -I, read 91s groups are unneeded and ignored. 91s 91s For both modes: 91s -M: path to a population map giving the list of samples 91s -O: output directory (default: none with -B; with -P same as the input 91s directory) 91s -t,--threads: number of threads to use (default: 1) 91s 91s SNP Model options: 91s --model: model to use to call variants and genotypes; one of 91s marukilow (default), marukihigh, or snp 91s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 91s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 91s 91s Paired-end options: 91s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 91s have the same insert length (implies --rm-unpaired-reads) 91s --rm-unpaired-reads: discard unpaired reads 91s --ignore-pe-reads: ignore paired-end reads even if present in the input 91s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 91s 91s Advanced options: 91s (De novo mode) 91s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 91s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 91s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 91s --write-alignments: save read alignments (heavy BAM files) 91s 91s (Reference-based mode) 91s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 91s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 91s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 91s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 91s 91s --details: write a heavier output 91s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 91s iterate over when building the graph of allele cooccurrences for 91s SNP phasing (default: 1,2) 91s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 91s genotypes during phasing 91s 91s kmer_filter 2.68 91s 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] 91s f: path to the input file if processing single-end seqeunces. 91s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 91s p: path to a directory of files (for single-end files only). 91s 1: specify the first in a pair of files to be processed together. 91s 2: specify the second in a pair of files to be processed together. 91s o: path to output the processed files. 91s y: output type, either 'fastq' or 'fasta' (default fastq). 91s D: capture discarded reads to a file. 91s h: display this help message. 91s 91s Filtering options: 91s --rare: turn on filtering based on rare k-mers. 91s --abundant: turn on filtering based on abundant k-mers. 91s --k-len : specify k-mer size (default 15). 91s 91s Advanced filtering options: 91s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 91s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 91s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 91s 91s Normalize data: 91s --normalize : normalize read depth according to k-mer coverage. 91s 91s Characterizing K-mers: 91s --write-k-freq: write kmers along with their frequency of occurrence and exit. 91s --k-dist: print k-mer frequency distribution and exit. 91s 91s Advanced input options: 91s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 91s 91s phasedstacks 2.68 91s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 91s b: Stacks batch ID. 91s P: path to the phased output files. 91s S: path to the Stacks output files. 91s t: input file type. Supported types: fastphase, and beagle. 91s p: number of processes to run in parallel sections of code. 91s M: path to the population map, a tab separated file describing which individuals belong in which population. 91s v: print program version. 91s h: display this help message. 91s --haplotypes: data were phased as RAD locus haplotypes. 91s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 91s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 91s 91s Filtering options: 91s --skip-zeros: do not include D' values of zero in the D' output. 91s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 91s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 91s 91s populations 2.68 91s Usage: 91s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 91s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 91s 91s -P,--in-path: path to a directory containing Stacks output files. 91s -V,--in-vcf: path to a standalone input VCF file. 91s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 91s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 91s -t,--threads: number of threads to run in parallel sections of code. 91s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 91s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 91s 91s Data Filtering: 91s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 91s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 91s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 91s -H,--filter-haplotype-wise: apply the above filters haplotype wise 91s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 91s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 91s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 91s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 91s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 91s 91s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 91s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 91s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 91s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 91s 91s Locus stats: 91s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 91s 91s Fstats: 91s --fstats: enable SNP and haplotype-based F statistics. 91s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 91s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 91s 91s Kernel-smoothing algorithm: 91s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 91s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 91s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 91s (Note: turning on smoothing implies --ordered-export.) 91s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 91s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 91s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 91s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 91s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 91s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 91s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 91s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 91s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 91s 91s File output options: 91s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 91s --fasta-loci: output locus consensus sequences in FASTA format. 91s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 91s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 91s --vcf-all: output all sites in Variant Call Format (VCF). 91s --genepop: output SNPs and haplotypes in GenePop format. 91s --structure: output results in Structure format. 91s --radpainter: output results in fineRADstructure/RADpainter format. 91s --plink: output genotypes in PLINK format. 91s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 91s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 91s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 91s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 91s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 91s --gtf: output locus positions in a GTF annotation file. 91s --no-hap-exports: omit haplotype outputs. 91s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 91s 91s Genetic map output options (population map must specify a genetic cross): 91s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 91s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 91s 91s Additional options: 91s -h,--help: display this help message. 91s -v,--version: print program version. 91s --verbose: turn on additional logging. 91s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 91s process_radtags 2.68 91s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 91s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 91s 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] 91s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 91s 91s -p,--in-path: path to a directory of files. 91s -P,--paired: files contained within the directory are paired. 91s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 91s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 91s -f: path to the input file if processing single-end sequences. 91s -1: first input file in a set of paired-end sequences. 91s -2: second input file in a set of paired-end sequences. 91s -o,--out-path: path to output the processed files. 91s --basename: specify the prefix of the output files when using -f or -1/-2. 91s 91s --threads: number of threads to run. 91s -c,--clean: clean data, remove any read with an uncalled base ('N'). 91s -q,--quality: discard reads with low quality (phred) scores. 91s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 91s -t,--truncate: truncate final read length to this value. 91s -D,--discards: capture discarded reads to a file. 91s 91s Barcode options: 91s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 91s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 91s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 91s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 91s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 91s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 91s --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). 91s 91s Restriction enzyme options: 91s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 91s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 91s Currently supported enzymes include: 91s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 91s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 91s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 91s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 91s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 91s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 91s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 91s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 91s 91s Protocol-specific options: 91s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 91s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 91s 91s Adapter options: 91s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 91s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 91s --adapter-mm : number of mismatches allowed in the adapter sequence. 91s 91s Input/Output options: 91s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 91s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 91s --retain-header: retain unmodified FASTQ headers in the output. 91s --merge: if no barcodes are specified, merge all input files into a single output file. 91s 91s Advanced options: 91s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 91s --disable-rad-check: disable checking if the RAD cut site is intact. 91s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 91s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 91s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 91s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 91s --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). 91s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 91s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 91s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 91s process_shortreads 2.68 91s 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] 91s f: path to the input file if processing single-end seqeunces. 91s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 91s p: path to a directory of single-end Illumina files. 91s 1: first input file in a set of paired-end sequences. 91s 2: second input file in a set of paired-end sequences. 91s P: specify that input is paired (for use with '-p'). 91s I: specify that the paired-end reads are interleaved in single files. 91s o: path to output the processed files. 91s y: output type, either 'fastq' or 'fasta' (default gzfastq). 91s b: a list of barcodes for this run. 91s c: clean data, remove any read with an uncalled base. 91s q: discard reads with low quality scores. 91s r: rescue barcodes. 91s t: truncate final read length to this value. 91s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 91s D: capture discarded reads to a file. 91s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 91s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 91s h: display this help message. 91s 91s Barcode options: 91s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 91s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 91s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 91s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 91s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 91s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 91s --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). 91s 91s Adapter options: 91s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 91s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 91s --adapter-mm : number of mismatches allowed in the adapter sequence. 91s 91s Output options: 91s --retain-header: retain unmodified FASTQ headers in the output. 91s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 91s 91s Advanced options: 91s --no-read-trimming: do not trim low quality reads, just discard them. 91s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 91s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 91s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 91s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 91s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 91s ref_map.pl 2.68 91s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 91s 91s Input/Output files: 91s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 91s --popmap: path to a population map file (format is " TAB ", one sample per line). 91s -s: spacer for file names: by default this is empty and the program looks for files 91s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 91s named 'SAMPLE_NAME.SPACER.bam'. 91s -o,--out-path: path to an output directory. 91s 91s General options: 91s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 91s -T: the number of threads/CPUs to use (default: 1). 91s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 91s that would be executed. 91s 91s SNP model options: 91s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 91s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 91s 91s Paired-end options: 91s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 91s the same insert length. 91s --ignore-pe-reads: ignore paired-end reads even if present in the input 91s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 91s 91s Population filtering options: 91s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 91s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 91s 91s Miscellaneous: 91s --time-components (for benchmarking) 91s sstacks 2.68 91s sstacks -P dir -M popmap [-t n_threads] 91s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 91s -P,--in-path: path to the directory containing Stacks files. 91s -M,--popmap: path to a population map file from which to take sample names. 91s -s,--sample: filename prefix from which to load sample loci. 91s -c,--catalog: path to the catalog. 91s -t,--threads: enable parallel execution with n_threads threads. 91s -o,--out-path: output path to write results. 91s -x: don't verify haplotype of matching locus. 91s 91s Gapped assembly options: 91s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 91s usage: 91s stacks-dist-extract logfile [section] 91s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 91s cat logfile | stacks-dist-extract [--pretty] [--section section] 91s 91s Export a paricular section of a Stacks log or distribs file. If you supply a 91s log path alone, stacks-dist-extract will print the available sections to 91s output. The log file can also be supplied via stdin. 91s 91s options: 91s -h, --help show this help message and exit 91s -p, --pretty Output data as a table with columns lined up. 91s -o, --out-path path Path to output file. 91s -s, --section section 91s Name of section to output from the log file. 91s Usage: 91s stacks-gdb PROGRAM ARGUMENTS 91s 91s e.g. 91s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 91s 91s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 91s case of a crash it will print additional information, helping us in fixing the 91s crash. 91s 91s This utility requires GDB, the GNU Debugger, to be installed on the system where 91s Stacks is run. You can check whether this is the case by just typing: 91s 91s gdb --version 91s 91s at the command prompt. Note that you may need to load the corresponding module. 91s GDB is standard scientific software, but may not be installed on some systems. 91s For further information please contact the administrators of your system; 91s trying to install GDB without administrator priviledges is not recommended. 91s 91s For questions please contact us, e.g. at stacks-users@googlegroups.com 91s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 91s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 91s [--version] 91s 91s Extracts the coordinates of the RAD loci from the given BAM file into a 91s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 91s 'catalog.calls' files so that they include the genomic coordinates given in 91s the input BAM file. 91s 91s options: 91s -h, --help show this help message and exit 91s -P, --in-path path Path to a directory containing Stacks ouput files. 91s -B, --bam-path path Path to a SAM or BAM file containing alignment of de 91s novo catalog loci to a reference genome. 91s -O, --out-path path Path to write the integrated ouput files. 91s -q, --min_mapq MIN_MAPQ 91s Minimum mapping quality as listed in the BAM file 91s (default 20). 91s -a, --min_alncov MIN_ALNCOV 91s Minimum fraction of the de novo catalog locus that 91s must participate in the alignment (default 0.6). 91s -p, --min_pctid MIN_PCTID 91s Minimum BLAST-style percent identity of the largest 91s alignment fragment for a de novo catalog locus 91s (default 0.6). 91s --verbose Provide verbose output. 91s --version show program's version number and exit 91s usage: 91s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 91s 91s Displays the read alignments of the given sample for the given locus, in text 91s format, to the standard output. Requires gstacks to have been run with the 91s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 91s tsv2bam 2.68 91s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 91s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 91s 91s -P,--in-dir: input directory. 91s -M,--popmap: population map. 91s -s,--sample: name of one sample. 91s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 91s -t: number of threads to use (default: 1). 91s 91s ustacks 2.68 91s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 91s -f,--file: input file path. 91s -o,--out-path: output path to write results. 91s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 91s -m: Minimum number of reads to seed a new stack (default 3). 91s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 91s -t,--threads: enable parallel execution with num_threads threads. 91s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 91s -n,--name: a name for the sample (default: input file name minus the suffix). 91s -R: retain unused reads. 91s -H: disable calling haplotypes from secondary reads. 91s 91s Stack assembly options: 91s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 91s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 91s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 91s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 91s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 91s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 91s 91s Gapped assembly options: 91s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 91s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 91s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 91s 91s Model options: 91s --model-type: either 'snp' (default), 'bounded', or 'fixed' 91s For the SNP or Bounded SNP model: 91s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 91s For the Bounded SNP model: 91s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 91s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 91s For the Fixed model: 91s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 91s 91s h: display this help message. 91s autopkgtest [23:02:38]: test run-unit-test: -----------------------] 92s run-unit-test PASS (superficial) 92s autopkgtest [23:02:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 92s autopkgtest [23:02:39]: @@@@@@@@@@@@@@@@@@@@ summary 92s run-unit-test PASS (superficial) 109s nova [W] Skipping flock for amd64 109s Creating nova instance adt-plucky-amd64-stacks-20250215-230106-juju-7f2275-prod-proposed-migration-environment-20-12949107-b6e5-422c-b45b-b1f3e38adf76 from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)... 109s nova [W] Timed out waiting for 333d5006-2bd1-486d-9583-6aa83ef029a6 to get deleted.