0s autopkgtest [17:57:51]: starting date and time: 2024-11-01 17:57:51+0000 0s autopkgtest [17:57:51]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [17:57:51]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0d8qcvuh/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib --apt-upgrade stacks --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-29.secgroup --name adt-plucky-arm64-stacks-20241101-175751-juju-7f2275-prod-proposed-migration-environment-15-34b88a45-4544-4fbd-9e91-ae50332c5f71 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 71s autopkgtest [17:59:02]: testbed dpkg architecture: arm64 71s autopkgtest [17:59:02]: testbed apt version: 2.9.8 71s autopkgtest [17:59:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 72s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 72s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [183 kB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2775 kB] 72s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 73s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [44.0 kB] 73s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [241 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [2023 kB] 73s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [36.5 kB] 73s Fetched 5433 kB in 1s (4290 kB/s) 73s Reading package lists... 75s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Calculating upgrade... 77s The following packages will be upgraded: 77s libevdev2 libftdi1-2 libinih1 nano python3-lazr.uri 77s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 374 kB of archives. 77s After this operation, 17.4 kB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B] 77s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB] 78s Fetched 374 kB in 0s (777 kB/s) 78s (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 ... 79705 files and directories currently installed.) 78s Preparing to unpack .../libevdev2_1.13.3+dfsg-1_arm64.deb ... 78s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 78s Preparing to unpack .../archives/nano_8.2-1_arm64.deb ... 78s Unpacking nano (8.2-1) over (8.1-1) ... 78s Preparing to unpack .../libftdi1-2_1.5-7_arm64.deb ... 78s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ... 78s Preparing to unpack .../libinih1_58-1ubuntu1_arm64.deb ... 78s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ... 78s Preparing to unpack .../python3-lazr.uri_1.0.6-4_all.deb ... 79s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 79s Setting up libinih1:arm64 (58-1ubuntu1) ... 79s Setting up python3-lazr.uri (1.0.6-4) ... 79s Setting up libftdi1-2:arm64 (1.5-7) ... 79s Setting up nano (8.2-1) ... 79s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ... 79s Processing triggers for man-db (2.12.1-3) ... 80s Processing triggers for install-info (7.1.1-1) ... 80s Processing triggers for libc-bin (2.40-1ubuntu3) ... 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 82s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 83s Reading package lists... 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 85s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [17:59:21]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 91s autopkgtest [17:59:22]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 92s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (dsc) [2041 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (tar) [348 kB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (diff) [12.2 kB] 93s gpgv: Signature made Sat Aug 10 12:47:16 2024 UTC 93s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 93s gpgv: Can't check signature: No public key 93s dpkg-source: warning: cannot verify inline signature for ./stacks_2.67+dfsg-1.dsc: no acceptable signature found 93s autopkgtest [17:59:24]: testing package stacks version 2.67+dfsg-1 93s autopkgtest [17:59:24]: build not needed 94s autopkgtest [17:59:25]: test run-unit-test: preparing testbed 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Starting pkgProblemResolver with broken count: 0 99s Starting 2 pkgProblemResolver with broken count: 0 99s Done 99s The following additional packages will be installed: 99s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 99s Suggested packages: 99s libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl cwltool 99s gdb 99s Recommended packages: 99s libspreadsheet-writeexcel-perl littler 99s The following NEW packages will be installed: 99s autopkgtest-satdep libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 99s samtools stacks 99s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 3155 kB/3156 kB of archives. 99s After this operation, 9856 kB of additional disk space will be used. 99s Get:1 /tmp/autopkgtest.jgey7w/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 100s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdbi-perl arm64 1.645-1 [826 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB] 100s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-7ubuntu1 [145 kB] 100s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB] 100s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB] 100s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB] 100s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 stacks arm64 2.67+dfsg-1 [1033 kB] 101s Fetched 3155 kB in 1s (4616 kB/s) 101s Selecting previously unselected package libdbi-perl:arm64. 101s (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 ... 79705 files and directories currently installed.) 101s Preparing to unpack .../0-libdbi-perl_1.645-1_arm64.deb ... 101s Unpacking libdbi-perl:arm64 (1.645-1) ... 101s Selecting previously unselected package libdeflate0:arm64. 101s Preparing to unpack .../1-libdeflate0_1.21-1_arm64.deb ... 101s Unpacking libdeflate0:arm64 (1.21-1) ... 101s Selecting previously unselected package libgomp1:arm64. 101s Preparing to unpack .../2-libgomp1_14.2.0-7ubuntu1_arm64.deb ... 101s Unpacking libgomp1:arm64 (14.2.0-7ubuntu1) ... 101s Selecting previously unselected package libhtscodecs2:arm64. 101s Preparing to unpack .../3-libhtscodecs2_1.6.0-1build1_arm64.deb ... 101s Unpacking libhtscodecs2:arm64 (1.6.0-1build1) ... 101s Selecting previously unselected package libhts3t64:arm64. 101s Preparing to unpack .../4-libhts3t64_1.20+ds-2_arm64.deb ... 101s Unpacking libhts3t64:arm64 (1.20+ds-2) ... 101s Selecting previously unselected package samtools. 101s Preparing to unpack .../5-samtools_1.20-3_arm64.deb ... 101s Unpacking samtools (1.20-3) ... 101s Selecting previously unselected package stacks. 101s Preparing to unpack .../6-stacks_2.67+dfsg-1_arm64.deb ... 101s Unpacking stacks (2.67+dfsg-1) ... 101s Selecting previously unselected package autopkgtest-satdep. 101s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 101s Unpacking autopkgtest-satdep (0) ... 101s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ... 101s Setting up libdeflate0:arm64 (1.21-1) ... 101s Setting up libgomp1:arm64 (14.2.0-7ubuntu1) ... 101s Setting up libhts3t64:arm64 (1.20+ds-2) ... 101s Setting up libdbi-perl:arm64 (1.645-1) ... 101s Setting up samtools (1.20-3) ... 101s Setting up stacks (2.67+dfsg-1) ... 101s Setting up autopkgtest-satdep (0) ... 101s Processing triggers for man-db (2.12.1-3) ... 102s Processing triggers for libc-bin (2.40-1ubuntu3) ... 105s (Reading database ... 80024 files and directories currently installed.) 105s Removing autopkgtest-satdep (0) ... 107s autopkgtest [17:59:38]: test run-unit-test: [----------------------- 107s Stacks - a pipeline for building loci from short-read sequences 107s v2.67+dfsg http://creskolab.uoregon.edu/stacks/ 107s 107s This is the Stacks wrapper script for Debian. Usage: 107s stacks 107s 107s Programs available are: 107s clone_filter ref_map 107s cstacks sstacks 107s denovo_map stacks-dist-extract 107s gstacks stacks-gdb 107s kmer_filter stacks-integrate-alignments 107s phasedstacks stacks-private-alleles 107s populations stacks-samtools-tview 107s process_radtags tsv2bam 107s process_shortreads ustacks 107s 107s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 107s 107s clone_filter 2.67 107s 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] 107s f: path to the input file if processing single-end sequences. 107s p: path to a directory of files. 107s P: files contained within directory specified by '-p' are paired. 107s 1: first input file in a set of paired-end sequences. 107s 2: second input file in a set of paired-end sequences. 107s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 107s o: path to output the processed files. 107s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 107s D: capture discarded reads to a file. 107s h: display this help message. 107s --oligo-len-1 len: length of the single-end oligo sequence in data set. 107s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 107s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 107s 107s Oligo sequence options: 107s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 107s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 107s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 107s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 107s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 107s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 107s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 107s --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). 107s 107s cstacks 2.67 107s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 107s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 107s 107s -P,--in-path: path to the directory containing Stacks files. 107s -M,--popmap: path to a population map file. 107s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 107s -t,--threads: enable parallel execution with num_threads threads. 107s -s: sample prefix from which to load loci into the catalog. 107s -o,--outpath: output path to write results. 107s -c,--catalog : add to an existing catalog. 107s 107s Gapped assembly options: 107s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 107s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 107s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 107s 107s Advanced options: 107s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 107s --report-mmatches: report query loci that match more than one catalog locus. 107s denovo_map.pl 2.67 107s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 107s 107s Input/Output files: 107s --samples: path to the directory containing the reads files for each sample. 107s --popmap: path to a population map file (format is " TAB ", one sample per line). 107s -o,--out-path: path to an output directory. 107s 107s General options: 107s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 107s -T, --threads: the number of threads/CPUs to use (default: 1). 107s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 107s --resume: resume executing the pipeline from a previous run. 107s 107s Stack assembly options: 107s -M: number of mismatches allowed between stacks within individuals (for ustacks). 107s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 107s 107s SNP model options: 107s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 107s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 107s 107s Paired-end options: 107s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 107s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 107s the same insert length. 107s 107s Population filtering options: 107s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 107s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 107s 107s For large datasets: 107s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 107s 107s Miscellaneous: 107s --time-components (for benchmarking) 108s gstacks 2.67 108s 108s De novo mode: 108s gstacks -P stacks_dir -M popmap 108s 108s -P: input directory containing '*.matches.bam' files created by the 108s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 108s 108s Reference-based mode: 108s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 108s gstacks -B bam_file [-B ...] -O out_dir 108s 108s -I: input directory containing BAM files 108s -S: with -I/-M, suffix to use to build BAM file names: by default this 108s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 108s -B: input BAM file(s) 108s 108s The input BAM file(s) must be sorted by coordinate. 108s With -B, records must be assigned to samples using BAM "reads groups" 108s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 108s must be consistent if repeated different files. Note that with -I, read 108s groups are unneeded and ignored. 108s 108s For both modes: 108s -M: path to a population map giving the list of samples 108s -O: output directory (default: none with -B; with -P same as the input 108s directory) 108s -t,--threads: number of threads to use (default: 1) 108s 108s SNP Model options: 108s --model: model to use to call variants and genotypes; one of 108s marukilow (default), marukihigh, or snp 108s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 108s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 108s 108s Paired-end options: 108s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 108s have the same insert length (implies --rm-unpaired-reads) 108s --rm-unpaired-reads: discard unpaired reads 108s --ignore-pe-reads: ignore paired-end reads even if present in the input 108s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 108s 108s Advanced options: 108s (De novo mode) 108s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 108s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 108s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 108s --write-alignments: save read alignments (heavy BAM files) 108s 108s (Reference-based mode) 108s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 108s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 108s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 108s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 108s 108s --details: write a heavier output 108s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 108s iterate over when building the graph of allele cooccurrences for 108s SNP phasing (default: 1,2) 108s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 108s genotypes during phasing 108s 108s kmer_filter 2.67 108s 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] 108s f: path to the input file if processing single-end seqeunces. 108s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 108s p: path to a directory of files (for single-end files only). 108s 1: specify the first in a pair of files to be processed together. 108s 2: specify the second in a pair of files to be processed together. 108s o: path to output the processed files. 108s y: output type, either 'fastq' or 'fasta' (default fastq). 108s D: capture discarded reads to a file. 108s h: display this help message. 108s 108s Filtering options: 108s --rare: turn on filtering based on rare k-mers. 108s --abundant: turn on filtering based on abundant k-mers. 108s --k-len : specify k-mer size (default 15). 108s 108s Advanced filtering options: 108s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 108s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 108s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 108s 108s Normalize data: 108s --normalize : normalize read depth according to k-mer coverage. 108s 108s Characterizing K-mers: 108s --write-k-freq: write kmers along with their frequency of occurrence and exit. 108s --k-dist: print k-mer frequency distribution and exit. 108s 108s Advanced input options: 108s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 108s 108s phasedstacks 2.67 108s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 108s b: Stacks batch ID. 108s P: path to the phased output files. 108s S: path to the Stacks output files. 108s t: input file type. Supported types: fastphase, and beagle. 108s p: number of processes to run in parallel sections of code. 108s M: path to the population map, a tab separated file describing which individuals belong in which population. 108s v: print program version. 108s h: display this help message. 108s --haplotypes: data were phased as RAD locus haplotypes. 108s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 108s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 108s 108s Filtering options: 108s --skip-zeros: do not include D' values of zero in the D' output. 108s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 108s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 108s 108s populations 2.67 108s Usage: 108s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 108s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 108s 108s -P,--in-path: path to a directory containing Stacks output files. 108s -V,--in-vcf: path to a standalone input VCF file. 108s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 108s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 108s -t,--threads: number of threads to run in parallel sections of code. 108s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 108s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 108s 108s Data Filtering: 108s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 108s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 108s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 108s -H,--filter-haplotype-wise: apply the above filters haplotype wise 108s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 108s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 108s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 108s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 108s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 108s 108s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 108s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 108s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 108s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 108s 108s Locus stats: 108s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 108s 108s Fstats: 108s --fstats: enable SNP and haplotype-based F statistics. 108s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 108s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 108s 108s Kernel-smoothing algorithm: 108s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 108s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 108s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 108s (Note: turning on smoothing implies --ordered-export.) 108s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 108s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 108s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 108s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 108s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 108s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 108s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 108s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 108s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 108s 108s File output options: 108s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 108s --fasta-loci: output locus consensus sequences in FASTA format. 108s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 108s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 108s --vcf-all: output all sites in Variant Call Format (VCF). 108s --genepop: output SNPs and haplotypes in GenePop format. 108s --structure: output results in Structure format. 108s --radpainter: output results in fineRADstructure/RADpainter format. 108s --plink: output genotypes in PLINK format. 108s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 108s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 108s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 108s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 108s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 108s --gtf: output locus positions in a GTF annotation file. 108s --no-hap-exports: omit haplotype outputs. 108s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 108s 108s Genetic map output options (population map must specify a genetic cross): 108s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 108s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 108s 108s Additional options: 108s -h,--help: display this help message. 108s -v,--version: print program version. 108s --verbose: turn on additional logging. 108s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 108s process_radtags 2.67 108s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 108s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 108s 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] 108s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 108s 108s -p,--in-path: path to a directory of files. 108s -P,--paired: files contained within the directory are paired. 108s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 108s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 108s -f: path to the input file if processing single-end sequences. 108s -1: first input file in a set of paired-end sequences. 108s -2: second input file in a set of paired-end sequences. 108s -o,--out-path: path to output the processed files. 108s --basename: specify the prefix of the output files when using -f or -1/-2. 108s 108s --threads: number of threads to run. 108s -c,--clean: clean data, remove any read with an uncalled base ('N'). 108s -q,--quality: discard reads with low quality (phred) scores. 108s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 108s -t,--truncate: truncate final read length to this value. 108s -D,--discards: capture discarded reads to a file. 108s 108s Barcode options: 108s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 108s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 108s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 108s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 108s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 108s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 108s --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). 108s 108s Restriction enzyme options: 108s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 108s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 108s Currently supported enzymes include: 108s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 108s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 108s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 108s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 108s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 108s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 108s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 108s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 108s 108s Protocol-specific options: 108s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 108s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 108s 108s Adapter options: 108s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 108s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 108s --adapter-mm : number of mismatches allowed in the adapter sequence. 108s 108s Input/Output options: 108s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 108s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 108s --retain-header: retain unmodified FASTQ headers in the output. 108s --merge: if no barcodes are specified, merge all input files into a single output file. 108s 108s Advanced options: 108s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 108s --disable-rad-check: disable checking if the RAD cut site is intact. 108s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 108s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 108s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 108s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 108s --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). 108s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 108s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 108s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 108s process_shortreads 2.67 108s 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] 108s f: path to the input file if processing single-end seqeunces. 108s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 108s p: path to a directory of single-end Illumina files. 108s 1: first input file in a set of paired-end sequences. 108s 2: second input file in a set of paired-end sequences. 108s P: specify that input is paired (for use with '-p'). 108s I: specify that the paired-end reads are interleaved in single files. 108s o: path to output the processed files. 108s y: output type, either 'fastq' or 'fasta' (default gzfastq). 108s b: a list of barcodes for this run. 108s c: clean data, remove any read with an uncalled base. 108s q: discard reads with low quality scores. 108s r: rescue barcodes. 108s t: truncate final read length to this value. 108s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 108s D: capture discarded reads to a file. 108s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 108s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 108s h: display this help message. 108s 108s Barcode options: 108s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 108s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 108s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 108s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 108s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 108s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 108s --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). 108s 108s Adapter options: 108s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 108s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 108s --adapter-mm : number of mismatches allowed in the adapter sequence. 108s 108s Output options: 108s --retain-header: retain unmodified FASTQ headers in the output. 108s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 108s 108s Advanced options: 108s --no-read-trimming: do not trim low quality reads, just discard them. 108s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 108s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 108s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 108s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 108s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 108s ref_map.pl 2.67 108s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 108s 108s Input/Output files: 108s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 108s --popmap: path to a population map file (format is " TAB ", one sample per line). 108s -s: spacer for file names: by default this is empty and the program looks for files 108s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 108s named 'SAMPLE_NAME.SPACER.bam'. 108s -o,--out-path: path to an output directory. 108s 108s General options: 108s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 108s -T: the number of threads/CPUs to use (default: 1). 108s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 108s that would be executed. 108s 108s SNP model options: 108s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 108s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 108s 108s Paired-end options: 108s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 108s the same insert length. 108s --ignore-pe-reads: ignore paired-end reads even if present in the input 108s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 108s 108s Population filtering options: 108s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 108s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 108s 108s Miscellaneous: 108s --time-components (for benchmarking) 108s sstacks 2.67 108s sstacks -P dir -M popmap [-t n_threads] 108s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 108s -P,--in-path: path to the directory containing Stacks files. 108s -M,--popmap: path to a population map file from which to take sample names. 108s -s,--sample: filename prefix from which to load sample loci. 108s -c,--catalog: path to the catalog. 108s -t,--threads: enable parallel execution with n_threads threads. 108s -o,--out-path: output path to write results. 108s -x: don't verify haplotype of matching locus. 108s 108s Gapped assembly options: 108s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 108s usage: 108s stacks-dist-extract logfile [section] 108s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 108s cat logfile | stacks-dist-extract [--pretty] [--section section] 108s 108s Export a paricular section of a Stacks log or distribs file. If you supply a 108s log path alone, stacks-dist-extract will print the available sections to 108s output. The log file can also be supplied via stdin. 108s 108s options: 108s -h, --help show this help message and exit 108s -p, --pretty Output data as a table with columns lined up. 108s -o path, --out-path path 108s Path to output file. 108s -s section, --section section 108s Name of section to output from the log file. 108s Usage: 108s stacks-gdb PROGRAM ARGUMENTS 108s 108s e.g. 108s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 108s 108s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 108s case of a crash it will print additional information, helping us in fixing the 108s crash. 108s 108s This utility requires GDB, the GNU Debugger, to be installed on the system where 108s Stacks is run. You can check whether this is the case by just typing: 108s 108s gdb --version 108s 108s at the command prompt. Note that you may need to load the corresponding module. 108s GDB is standard scientific software, but may not be installed on some systems. 108s For further information please contact the administrators of your system; 108s trying to install GDB without administrator priviledges is not recommended. 108s 108s For questions please contact us, e.g. at stacks-users@googlegroups.com 108s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 108s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 108s [--version] 108s 108s Extracts the coordinates of the RAD loci from the given BAM file into a 108s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 108s 'catalog.calls' files so that they include the genomic coordinates given in 108s the input BAM file. 108s 108s options: 108s -h, --help show this help message and exit 108s -P path, --in-path path 108s Path to a directory containing Stacks ouput files. 108s -B path, --bam-path path 108s Path to a SAM or BAM file containing alignment of de 108s novo catalog loci to a reference genome. 108s -O path, --out-path path 108s Path to write the integrated ouput files. 108s -q MIN_MAPQ, --min_mapq MIN_MAPQ 108s Minimum mapping quality as listed in the BAM file 108s (default 20). 108s -a MIN_ALNCOV, --min_alncov MIN_ALNCOV 108s Minimum fraction of the de novo catalog locus that 108s must participate in the alignment (default 0.6). 108s -p MIN_PCTID, --min_pctid MIN_PCTID 108s Minimum BLAST-style percent identity of the largest 108s alignment fragment for a de novo catalog locus 108s (default 0.6). 108s --verbose Provide verbose output. 108s --version show program's version number and exit 108s usage: 108s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 108s 108s Displays the read alignments of the given sample for the given locus, in text 108s format, to the standard output. Requires gstacks to have been run with the 108s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 108s tsv2bam 2.67 108s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 108s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 108s 108s -P,--in-dir: input directory. 108s -M,--popmap: population map. 108s -s,--sample: name of one sample. 108s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 108s -t: number of threads to use (default: 1). 108s 108s ustacks 2.67 108s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 108s -f,--file: input file path. 108s -o,--out-path: output path to write results. 108s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 108s -m: Minimum number of reads to seed a new stack (default 3). 108s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 108s -t,--threads: enable parallel execution with num_threads threads. 108s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 108s -n,--name: a name for the sample (default: input file name minus the suffix). 108s -R: retain unused reads. 108s -H: disable calling haplotypes from secondary reads. 108s 108s Stack assembly options: 108s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 108s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 108s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 108s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 108s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 108s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 108s 108s Gapped assembly options: 108s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 108s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 108s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 108s 108s Model options: 108s --model-type: either 'snp' (default), 'bounded', or 'fixed' 108s For the SNP or Bounded SNP model: 108s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 108s For the Bounded SNP model: 108s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 108s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 108s For the Fixed model: 108s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 108s 108s h: display this help message. 108s autopkgtest [17:59:39]: test run-unit-test: -----------------------] 109s autopkgtest [17:59:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 109s run-unit-test PASS (superficial) 109s autopkgtest [17:59:40]: @@@@@@@@@@@@@@@@@@@@ summary 109s run-unit-test PASS (superficial) 121s nova [W] Skipping flock in bos03-arm64 121s Creating nova instance adt-plucky-arm64-stacks-20241101-175751-juju-7f2275-prod-proposed-migration-environment-15-34b88a45-4544-4fbd-9e91-ae50332c5f71 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...