0s autopkgtest [17:51:12]: starting date and time: 2025-03-15 17:51:12+0000 0s autopkgtest [17:51:12]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:51:12]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s_9cysra/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade stacks --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.201 lxd-armhf-10.145.243.201:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [17:51:32]: testbed dpkg architecture: armhf 22s autopkgtest [17:51:34]: testbed apt version: 2.9.33 26s autopkgtest [17:51:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [17:51:39]: testbed release detected to be: None 35s autopkgtest [17:51:47]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 37s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 38s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 38s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 38s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 38s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 38s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 39s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 58s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 59s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 60s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 74s Get:20 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 76s Fetched 40.7 MB in 38s (1065 kB/s) 77s Reading package lists... 83s autopkgtest [17:52:35]: upgrading testbed (apt dist-upgrade and autopurge) 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 85s Starting 2 pkgProblemResolver with broken count: 0 86s Done 86s Entering ResolveByKeep 86s 87s Calculating upgrade... 87s The following packages will be upgraded: 87s libc-bin libc6 locales pinentry-curses sos 87s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Need to get 8128 kB of archives. 87s After this operation, 0 B of additional disk space will be used. 87s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 90s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 91s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 95s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 95s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 96s Preconfiguring packages ... 96s Fetched 8128 kB in 8s (1006 kB/s) 96s (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 ... 64655 files and directories currently installed.) 96s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 96s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Setting up libc6:armhf (2.41-1ubuntu2) ... 96s (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 ... 64655 files and directories currently installed.) 96s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 96s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Setting up libc-bin (2.41-1ubuntu2) ... 97s (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 ... 64655 files and directories currently installed.) 97s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 97s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 97s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 97s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 97s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 97s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 97s Setting up sos (4.9.0-5) ... 98s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 98s Setting up locales (2.41-1ubuntu2) ... 99s Generating locales (this might take a while)... 101s en_US.UTF-8... done 101s Generation complete. 101s Processing triggers for systemd (257.3-1ubuntu3) ... 101s Processing triggers for man-db (2.13.0-1) ... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Starting pkgProblemResolver with broken count: 0 105s Starting 2 pkgProblemResolver with broken count: 0 105s Done 105s Solving dependencies... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [17:53:00]: rebooting testbed after setup commands that affected boot 149s autopkgtest [17:53:41]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 174s autopkgtest [17:54:06]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 185s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (dsc) [2050 B] 185s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (tar) [371 kB] 185s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.68+dfsg-2 (diff) [12.5 kB] 185s gpgv: Signature made Sun Feb 16 10:21:57 2025 UTC 185s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 185s gpgv: issuer "emollier@debian.org" 185s gpgv: Can't check signature: No public key 185s dpkg-source: warning: cannot verify inline signature for ./stacks_2.68+dfsg-2.dsc: no acceptable signature found 185s autopkgtest [17:54:17]: testing package stacks version 2.68+dfsg-2 187s autopkgtest [17:54:19]: build not needed 189s autopkgtest [17:54:21]: test run-unit-test: preparing testbed 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 192s Starting 2 pkgProblemResolver with broken count: 0 192s Done 193s The following NEW packages will be installed: 193s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 193s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 193s Need to get 3271 kB of archives. 193s After this operation, 9771 kB of additional disk space will be used. 193s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libdbi-perl armhf 1.647-1 [823 kB] 194s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 194s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 194s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 195s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.21-1 [619 kB] 195s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf stacks armhf 2.68+dfsg-2 [1196 kB] 197s Fetched 3271 kB in 4s (774 kB/s) 197s Selecting previously unselected package libdbi-perl:armhf. 197s (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 ... 64655 files and directories currently installed.) 197s Preparing to unpack .../0-libdbi-perl_1.647-1_armhf.deb ... 197s Unpacking libdbi-perl:armhf (1.647-1) ... 197s Selecting previously unselected package libdeflate0:armhf. 197s Preparing to unpack .../1-libdeflate0_1.23-1_armhf.deb ... 197s Unpacking libdeflate0:armhf (1.23-1) ... 197s Selecting previously unselected package libgomp1:armhf. 197s Preparing to unpack .../2-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 197s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 197s Selecting previously unselected package libhtscodecs2:armhf. 198s Preparing to unpack .../3-libhtscodecs2_1.6.1-2_armhf.deb ... 198s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 198s Selecting previously unselected package libhts3t64:armhf. 198s Preparing to unpack .../4-libhts3t64_1.21+ds-1_armhf.deb ... 198s Unpacking libhts3t64:armhf (1.21+ds-1) ... 198s Selecting previously unselected package samtools. 198s Preparing to unpack .../5-samtools_1.21-1_armhf.deb ... 198s Unpacking samtools (1.21-1) ... 198s Selecting previously unselected package stacks. 198s Preparing to unpack .../6-stacks_2.68+dfsg-2_armhf.deb ... 198s Unpacking stacks (2.68+dfsg-2) ... 198s Setting up libhtscodecs2:armhf (1.6.1-2) ... 198s Setting up libdeflate0:armhf (1.23-1) ... 198s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 198s Setting up libhts3t64:armhf (1.21+ds-1) ... 198s Setting up libdbi-perl:armhf (1.647-1) ... 198s Setting up samtools (1.21-1) ... 198s Setting up stacks (2.68+dfsg-2) ... 198s Processing triggers for man-db (2.13.0-1) ... 198s Processing triggers for libc-bin (2.41-1ubuntu2) ... 207s autopkgtest [17:54:39]: test run-unit-test: [----------------------- 209s Stacks - a pipeline for building loci from short-read sequences 209s v2.68+dfsg http://creskolab.uoregon.edu/stacks/ 209s 209s This is the Stacks wrapper script for Debian. Usage: 209s stacks 209s 209s Programs available are: 209s clone_filter ref_map 209s cstacks sstacks 209s denovo_map stacks-dist-extract 209s gstacks stacks-gdb 209s kmer_filter stacks-integrate-alignments 209s phasedstacks stacks-private-alleles 209s populations stacks-samtools-tview 209s process_radtags tsv2bam 209s process_shortreads ustacks 209s 209s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 209s 209s clone_filter 2.68 209s 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] 209s f: path to the input file if processing single-end sequences. 209s p: path to a directory of files. 209s P: files contained within directory specified by '-p' are paired. 209s 1: first input file in a set of paired-end sequences. 209s 2: second input file in a set of paired-end sequences. 209s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 209s o: path to output the processed files. 209s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 209s D: capture discarded reads to a file. 209s h: display this help message. 209s --oligo-len-1 len: length of the single-end oligo sequence in data set. 209s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 209s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 209s 209s Oligo sequence options: 209s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 209s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 209s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 209s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 209s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 209s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 209s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 209s --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). 209s 209s cstacks 2.68 209s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 209s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 209s 209s -P,--in-path: path to the directory containing Stacks files. 209s -M,--popmap: path to a population map file. 209s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 209s -t,--threads: enable parallel execution with num_threads threads. 209s -s: sample prefix from which to load loci into the catalog. 209s -o,--outpath: output path to write results. 209s -c,--catalog : add to an existing catalog. 209s 209s Gapped assembly options: 209s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 209s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 209s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 209s 209s Advanced options: 209s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 209s --report-mmatches: report query loci that match more than one catalog locus. 209s denovo_map.pl 2.68 209s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 209s 209s Input/Output files: 209s --samples: path to the directory containing the reads files for each sample. 209s --popmap: path to a population map file (format is " TAB ", one sample per line). 209s -o,--out-path: path to an output directory. 209s 209s General options: 209s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 209s -T, --threads: the number of threads/CPUs to use (default: 1). 209s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 209s --resume: resume executing the pipeline from a previous run. 209s 209s Stack assembly options: 209s -M: number of mismatches allowed between stacks within individuals (for ustacks). 209s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 209s 209s SNP model options: 209s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 209s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 209s 209s Paired-end options: 209s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 209s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 209s the same insert length. 209s 209s Population filtering options: 209s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 209s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 209s 209s For large datasets: 209s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 209s 209s Miscellaneous: 209s --time-components (for benchmarking) 209s gstacks 2.68 209s 209s De novo mode: 209s gstacks -P stacks_dir -M popmap 209s 209s -P: input directory containing '*.matches.bam' files created by the 209s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 209s 209s Reference-based mode: 209s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 209s gstacks -B bam_file [-B ...] -O out_dir 209s 209s -I: input directory containing BAM files 209s -S: with -I/-M, suffix to use to build BAM file names: by default this 209s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 209s -B: input BAM file(s) 209s 209s The input BAM file(s) must be sorted by coordinate. 209s With -B, records must be assigned to samples using BAM "reads groups" 209s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 209s must be consistent if repeated different files. Note that with -I, read 209s groups are unneeded and ignored. 209s 209s For both modes: 209s -M: path to a population map giving the list of samples 209s -O: output directory (default: none with -B; with -P same as the input 209s directory) 209s -t,--threads: number of threads to use (default: 1) 209s 209s SNP Model options: 209s --model: model to use to call variants and genotypes; one of 209s marukilow (default), marukihigh, or snp 209s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 209s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 209s 209s Paired-end options: 209s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 209s have the same insert length (implies --rm-unpaired-reads) 209s --rm-unpaired-reads: discard unpaired reads 209s --ignore-pe-reads: ignore paired-end reads even if present in the input 209s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 209s 209s Advanced options: 209s (De novo mode) 209s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 209s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 209s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 209s --write-alignments: save read alignments (heavy BAM files) 209s 209s (Reference-based mode) 209s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 209s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 209s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 209s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 209s 209s --details: write a heavier output 209s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 209s iterate over when building the graph of allele cooccurrences for 209s SNP phasing (default: 1,2) 209s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 209s genotypes during phasing 209s 209s kmer_filter 2.68 209s 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] 209s f: path to the input file if processing single-end seqeunces. 209s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 209s p: path to a directory of files (for single-end files only). 209s 1: specify the first in a pair of files to be processed together. 209s 2: specify the second in a pair of files to be processed together. 209s o: path to output the processed files. 209s y: output type, either 'fastq' or 'fasta' (default fastq). 209s D: capture discarded reads to a file. 209s h: display this help message. 209s 209s Filtering options: 209s --rare: turn on filtering based on rare k-mers. 209s --abundant: turn on filtering based on abundant k-mers. 209s --k-len : specify k-mer size (default 15). 209s 209s Advanced filtering options: 209s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 209s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 209s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 209s 209s Normalize data: 209s --normalize : normalize read depth according to k-mer coverage. 209s 209s Characterizing K-mers: 209s --write-k-freq: write kmers along with their frequency of occurrence and exit. 209s --k-dist: print k-mer frequency distribution and exit. 209s 209s Advanced input options: 209s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 209s 209s phasedstacks 2.68 209s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 209s b: Stacks batch ID. 209s P: path to the phased output files. 209s S: path to the Stacks output files. 209s t: input file type. Supported types: fastphase, and beagle. 209s p: number of processes to run in parallel sections of code. 209s M: path to the population map, a tab separated file describing which individuals belong in which population. 209s v: print program version. 209s h: display this help message. 209s --haplotypes: data were phased as RAD locus haplotypes. 209s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 209s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 209s 209s Filtering options: 209s --skip-zeros: do not include D' values of zero in the D' output. 209s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 209s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 209s 209s populations 2.68 209s Usage: 209s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 209s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 209s 209s -P,--in-path: path to a directory containing Stacks output files. 209s -V,--in-vcf: path to a standalone input VCF file. 209s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 209s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 209s -t,--threads: number of threads to run in parallel sections of code. 209s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 209s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 209s 209s Data Filtering: 209s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 209s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 209s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 209s -H,--filter-haplotype-wise: apply the above filters haplotype wise 209s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 209s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 209s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 209s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 209s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 209s 209s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 209s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 209s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 209s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 209s 209s Locus stats: 209s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 209s 209s Fstats: 209s --fstats: enable SNP and haplotype-based F statistics. 209s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 209s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 209s 209s Kernel-smoothing algorithm: 209s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 209s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 209s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 209s (Note: turning on smoothing implies --ordered-export.) 209s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 209s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 209s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 209s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 209s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 209s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 209s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 209s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 209s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 209s 209s File output options: 209s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 209s --fasta-loci: output locus consensus sequences in FASTA format. 209s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 209s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 209s --vcf-all: output all sites in Variant Call Format (VCF). 209s --genepop: output SNPs and haplotypes in GenePop format. 209s --structure: output results in Structure format. 209s --radpainter: output results in fineRADstructure/RADpainter format. 209s --plink: output genotypes in PLINK format. 209s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 209s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 209s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 209s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 209s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 209s --gtf: output locus positions in a GTF annotation file. 209s --no-hap-exports: omit haplotype outputs. 209s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 209s 209s Genetic map output options (population map must specify a genetic cross): 209s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 209s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 209s 209s Additional options: 209s -h,--help: display this help message. 209s -v,--version: print program version. 209s --verbose: turn on additional logging. 209s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 209s process_radtags 2.68 209s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 209s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 209s 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] 209s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 209s 209s -p,--in-path: path to a directory of files. 209s -P,--paired: files contained within the directory are paired. 209s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 209s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 209s -f: path to the input file if processing single-end sequences. 209s -1: first input file in a set of paired-end sequences. 209s -2: second input file in a set of paired-end sequences. 209s -o,--out-path: path to output the processed files. 209s --basename: specify the prefix of the output files when using -f or -1/-2. 209s 209s --threads: number of threads to run. 209s -c,--clean: clean data, remove any read with an uncalled base ('N'). 209s -q,--quality: discard reads with low quality (phred) scores. 209s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 209s -t,--truncate: truncate final read length to this value. 209s -D,--discards: capture discarded reads to a file. 209s 209s Barcode options: 209s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 209s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 209s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 209s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 209s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 209s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 209s --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). 209s 209s Restriction enzyme options: 209s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 209s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 209s Currently supported enzymes include: 209s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 209s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 209s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 209s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 209s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 209s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 209s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 209s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 209s 209s Protocol-specific options: 209s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 209s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 209s 209s Adapter options: 209s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 209s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 209s --adapter-mm : number of mismatches allowed in the adapter sequence. 209s 209s Input/Output options: 209s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 209s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 209s --retain-header: retain unmodified FASTQ headers in the output. 209s --merge: if no barcodes are specified, merge all input files into a single output file. 209s 209s Advanced options: 209s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 209s --disable-rad-check: disable checking if the RAD cut site is intact. 209s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 209s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 209s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 209s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 209s --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). 209s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 209s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 209s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 209s process_shortreads 2.68 209s 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] 209s f: path to the input file if processing single-end seqeunces. 209s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 209s p: path to a directory of single-end Illumina files. 209s 1: first input file in a set of paired-end sequences. 209s 2: second input file in a set of paired-end sequences. 209s P: specify that input is paired (for use with '-p'). 209s I: specify that the paired-end reads are interleaved in single files. 209s o: path to output the processed files. 209s y: output type, either 'fastq' or 'fasta' (default gzfastq). 209s b: a list of barcodes for this run. 209s c: clean data, remove any read with an uncalled base. 209s q: discard reads with low quality scores. 209s r: rescue barcodes. 209s t: truncate final read length to this value. 209s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 209s D: capture discarded reads to a file. 209s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 209s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 209s h: display this help message. 209s 209s Barcode options: 209s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 209s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 209s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 209s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 209s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 209s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 209s --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). 209s 209s Adapter options: 209s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 209s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 209s --adapter-mm : number of mismatches allowed in the adapter sequence. 209s 209s Output options: 209s --retain-header: retain unmodified FASTQ headers in the output. 209s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 209s 209s Advanced options: 209s --no-read-trimming: do not trim low quality reads, just discard them. 209s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 209s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 209s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 209s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 209s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 209s ref_map.pl 2.68 209s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 209s 209s Input/Output files: 209s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 209s --popmap: path to a population map file (format is " TAB ", one sample per line). 209s -s: spacer for file names: by default this is empty and the program looks for files 209s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 209s named 'SAMPLE_NAME.SPACER.bam'. 209s -o,--out-path: path to an output directory. 209s 209s General options: 209s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 209s -T: the number of threads/CPUs to use (default: 1). 209s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 209s that would be executed. 209s 209s SNP model options: 209s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 209s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 209s 209s Paired-end options: 209s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 209s the same insert length. 209s --ignore-pe-reads: ignore paired-end reads even if present in the input 209s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 209s 209s Population filtering options: 209s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 209s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 209s 209s Miscellaneous: 209s --time-components (for benchmarking) 209s sstacks 2.68 209s sstacks -P dir -M popmap [-t n_threads] 209s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 209s -P,--in-path: path to the directory containing Stacks files. 209s -M,--popmap: path to a population map file from which to take sample names. 209s -s,--sample: filename prefix from which to load sample loci. 209s -c,--catalog: path to the catalog. 209s -t,--threads: enable parallel execution with n_threads threads. 209s -o,--out-path: output path to write results. 209s -x: don't verify haplotype of matching locus. 209s 209s Gapped assembly options: 209s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 209s usage: 209s stacks-dist-extract logfile [section] 209s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 209s cat logfile | stacks-dist-extract [--pretty] [--section section] 209s 209s Export a paricular section of a Stacks log or distribs file. If you supply a 209s log path alone, stacks-dist-extract will print the available sections to 209s output. The log file can also be supplied via stdin. 209s 209s options: 209s -h, --help show this help message and exit 209s -p, --pretty Output data as a table with columns lined up. 209s -o, --out-path path Path to output file. 209s -s, --section section 209s Name of section to output from the log file. 209s Usage: 209s stacks-gdb PROGRAM ARGUMENTS 209s 209s e.g. 209s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 209s 209s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 209s case of a crash it will print additional information, helping us in fixing the 209s crash. 209s 209s This utility requires GDB, the GNU Debugger, to be installed on the system where 209s Stacks is run. You can check whether this is the case by just typing: 209s 209s gdb --version 209s 209s at the command prompt. Note that you may need to load the corresponding module. 209s GDB is standard scientific software, but may not be installed on some systems. 209s For further information please contact the administrators of your system; 209s trying to install GDB without administrator priviledges is not recommended. 209s 209s For questions please contact us, e.g. at stacks-users@googlegroups.com 209s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 209s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 209s [--version] 209s 209s Extracts the coordinates of the RAD loci from the given BAM file into a 209s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 209s 'catalog.calls' files so that they include the genomic coordinates given in 209s the input BAM file. 209s 209s options: 209s -h, --help show this help message and exit 209s -P, --in-path path Path to a directory containing Stacks ouput files. 209s -B, --bam-path path Path to a SAM or BAM file containing alignment of de 209s novo catalog loci to a reference genome. 209s -O, --out-path path Path to write the integrated ouput files. 209s -q, --min_mapq MIN_MAPQ 209s Minimum mapping quality as listed in the BAM file 209s (default 20). 209s -a, --min_alncov MIN_ALNCOV 209s Minimum fraction of the de novo catalog locus that 209s must participate in the alignment (default 0.6). 209s -p, --min_pctid MIN_PCTID 209s Minimum BLAST-style percent identity of the largest 209s alignment fragment for a de novo catalog locus 209s (default 0.6). 209s --verbose Provide verbose output. 209s --version show program's version number and exit 209s usage: 209s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 209s 209s Displays the read alignments of the given sample for the given locus, in text 209s format, to the standard output. Requires gstacks to have been run with the 209s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 209s tsv2bam 2.68 209s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 209s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 209s 209s -P,--in-dir: input directory. 209s -M,--popmap: population map. 209s -s,--sample: name of one sample. 209s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 209s -t: number of threads to use (default: 1). 209s 209s ustacks 2.68 209s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 209s -f,--file: input file path. 209s -o,--out-path: output path to write results. 209s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 209s -m: Minimum number of reads to seed a new stack (default 3). 209s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 209s -t,--threads: enable parallel execution with num_threads threads. 209s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 209s -n,--name: a name for the sample (default: input file name minus the suffix). 209s -R: retain unused reads. 209s -H: disable calling haplotypes from secondary reads. 209s 209s Stack assembly options: 209s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 209s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 209s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 209s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 209s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 209s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 209s 209s Gapped assembly options: 209s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 209s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 209s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 209s 209s Model options: 209s --model-type: either 'snp' (default), 'bounded', or 'fixed' 209s For the SNP or Bounded SNP model: 209s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 209s For the Bounded SNP model: 209s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 209s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 209s For the Fixed model: 209s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 209s 209s h: display this help message. 209s autopkgtest [17:54:41]: test run-unit-test: -----------------------] 213s autopkgtest [17:54:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 213s run-unit-test PASS (superficial) 217s autopkgtest [17:54:49]: @@@@@@@@@@@@@@@@@@@@ summary 217s run-unit-test PASS (superficial)