0s autopkgtest [07:43:09]: starting date and time: 2024-11-03 07:43:09+0000 0s autopkgtest [07:43:09]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [07:43:09]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3ok445i_/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-2.secgroup --name adt-plucky-ppc64el-stacks-20241103-074309-juju-7f2275-prod-proposed-migration-environment-15-a4dcec1c-5be6-4ab6-b897-3a199f6b76d2 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 120s autopkgtest [07:45:09]: testbed dpkg architecture: ppc64el 120s autopkgtest [07:45:09]: testbed apt version: 2.9.8 120s autopkgtest [07:45:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 121s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 121s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 122s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 122s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 122s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 122s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [213 kB] 122s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [1576 kB] 122s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [37.8 kB] 122s Fetched 4384 kB in 2s (2842 kB/s) 123s Reading package lists... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 127s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 128s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Calculating upgrade... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s autopkgtest [07:45:22]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 133s autopkgtest [07:45:22]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 135s Get:1 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (dsc) [2041 B] 135s Get:2 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (tar) [348 kB] 135s Get:3 http://ftpmaster.internal/ubuntu plucky/universe stacks 2.67+dfsg-1 (diff) [12.2 kB] 135s gpgv: Signature made Sat Aug 10 12:47:16 2024 UTC 135s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 135s gpgv: Can't check signature: No public key 135s dpkg-source: warning: cannot verify inline signature for ./stacks_2.67+dfsg-1.dsc: no acceptable signature found 136s autopkgtest [07:45:25]: testing package stacks version 2.67+dfsg-1 136s autopkgtest [07:45:25]: build not needed 137s autopkgtest [07:45:26]: test run-unit-test: preparing testbed 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 139s The following additional packages will be installed: 139s libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 samtools stacks 139s Suggested packages: 139s libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl cwltool 139s gdb 139s Recommended packages: 139s libspreadsheet-writeexcel-perl littler 139s The following NEW packages will be installed: 139s autopkgtest-satdep libdbi-perl libdeflate0 libgomp1 libhts3t64 libhtscodecs2 139s samtools stacks 139s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 3595 kB/3596 kB of archives. 139s After this operation, 11.8 MB of additional disk space will be used. 139s Get:1 /tmp/autopkgtest.hiUzE3/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdbi-perl ppc64el 1.645-1 [837 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.21-1 [63.3 kB] 140s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-7ubuntu1 [161 kB] 140s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1build1 [110 kB] 140s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el libhts3t64 ppc64el 1.20+ds-2 [574 kB] 140s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.20-3 [676 kB] 140s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el stacks ppc64el 2.67+dfsg-1 [1175 kB] 140s Fetched 3595 kB in 1s (5287 kB/s) 140s Selecting previously unselected package libdbi-perl:ppc64el. 141s (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 ... 73549 files and directories currently installed.) 141s Preparing to unpack .../0-libdbi-perl_1.645-1_ppc64el.deb ... 141s Unpacking libdbi-perl:ppc64el (1.645-1) ... 141s Selecting previously unselected package libdeflate0:ppc64el. 141s Preparing to unpack .../1-libdeflate0_1.21-1_ppc64el.deb ... 141s Unpacking libdeflate0:ppc64el (1.21-1) ... 141s Selecting previously unselected package libgomp1:ppc64el. 141s Preparing to unpack .../2-libgomp1_14.2.0-7ubuntu1_ppc64el.deb ... 141s Unpacking libgomp1:ppc64el (14.2.0-7ubuntu1) ... 141s Selecting previously unselected package libhtscodecs2:ppc64el. 141s Preparing to unpack .../3-libhtscodecs2_1.6.0-1build1_ppc64el.deb ... 141s Unpacking libhtscodecs2:ppc64el (1.6.0-1build1) ... 141s Selecting previously unselected package libhts3t64:ppc64el. 141s Preparing to unpack .../4-libhts3t64_1.20+ds-2_ppc64el.deb ... 141s Unpacking libhts3t64:ppc64el (1.20+ds-2) ... 141s Selecting previously unselected package samtools. 141s Preparing to unpack .../5-samtools_1.20-3_ppc64el.deb ... 141s Unpacking samtools (1.20-3) ... 141s Selecting previously unselected package stacks. 141s Preparing to unpack .../6-stacks_2.67+dfsg-1_ppc64el.deb ... 141s Unpacking stacks (2.67+dfsg-1) ... 141s Selecting previously unselected package autopkgtest-satdep. 141s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 141s Unpacking autopkgtest-satdep (0) ... 141s Setting up libhtscodecs2:ppc64el (1.6.0-1build1) ... 141s Setting up libdeflate0:ppc64el (1.21-1) ... 141s Setting up libgomp1:ppc64el (14.2.0-7ubuntu1) ... 141s Setting up libhts3t64:ppc64el (1.20+ds-2) ... 141s Setting up libdbi-perl:ppc64el (1.645-1) ... 141s Setting up samtools (1.20-3) ... 141s Setting up stacks (2.67+dfsg-1) ... 141s Setting up autopkgtest-satdep (0) ... 141s Processing triggers for man-db (2.12.1-3) ... 142s Processing triggers for libc-bin (2.40-1ubuntu3) ... 144s (Reading database ... 73868 files and directories currently installed.) 144s Removing autopkgtest-satdep (0) ... 145s autopkgtest [07:45:34]: test run-unit-test: [----------------------- 146s Stacks - a pipeline for building loci from short-read sequences 146s v2.67+dfsg http://creskolab.uoregon.edu/stacks/ 146s 146s This is the Stacks wrapper script for Debian. Usage: 146s stacks 146s 146s Programs available are: 146s clone_filter ref_map 146s cstacks sstacks 146s denovo_map stacks-dist-extract 146s gstacks stacks-gdb 146s kmer_filter stacks-integrate-alignments 146s phasedstacks stacks-private-alleles 146s populations stacks-samtools-tview 146s process_radtags tsv2bam 146s process_shortreads ustacks 146s 146s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 146s 146s clone_filter 2.67 146s 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] 146s f: path to the input file if processing single-end sequences. 146s p: path to a directory of files. 146s P: files contained within directory specified by '-p' are paired. 146s 1: first input file in a set of paired-end sequences. 146s 2: second input file in a set of paired-end sequences. 146s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 146s o: path to output the processed files. 146s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 146s D: capture discarded reads to a file. 146s h: display this help message. 146s --oligo-len-1 len: length of the single-end oligo sequence in data set. 146s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 146s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 146s 146s Oligo sequence options: 146s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 146s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 146s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 146s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 146s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 146s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 146s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 146s --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). 146s 146s cstacks 2.67 146s cstacks -P in_dir -M popmap [-n num_mismatches] [-t num_threads] 146s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-t num_threads] 146s 146s -P,--in-path: path to the directory containing Stacks files. 146s -M,--popmap: path to a population map file. 146s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 146s -t,--threads: enable parallel execution with num_threads threads. 146s -s: sample prefix from which to load loci into the catalog. 146s -o,--outpath: output path to write results. 146s -c,--catalog : add to an existing catalog. 146s 146s Gapped assembly options: 146s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 146s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 146s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 146s 146s Advanced options: 146s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 146s --report-mmatches: report query loci that match more than one catalog locus. 146s denovo_map.pl 2.67 146s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 146s 146s Input/Output files: 146s --samples: path to the directory containing the reads files for each sample. 146s --popmap: path to a population map file (format is " TAB ", one sample per line). 146s -o,--out-path: path to an output directory. 146s 146s General options: 146s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 146s -T, --threads: the number of threads/CPUs to use (default: 1). 146s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 146s --resume: resume executing the pipeline from a previous run. 146s 146s Stack assembly options: 146s -M: number of mismatches allowed between stacks within individuals (for ustacks). 146s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 146s 146s SNP model options: 146s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 146s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 146s 146s Paired-end options: 146s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 146s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 146s the same insert length. 146s 146s Population filtering options: 146s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 146s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 146s 146s For large datasets: 146s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 146s 146s Miscellaneous: 146s --time-components (for benchmarking) 146s gstacks 2.67 146s 146s De novo mode: 146s gstacks -P stacks_dir -M popmap 146s 146s -P: input directory containing '*.matches.bam' files created by the 146s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 146s 146s Reference-based mode: 146s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 146s gstacks -B bam_file [-B ...] -O out_dir 146s 146s -I: input directory containing BAM files 146s -S: with -I/-M, suffix to use to build BAM file names: by default this 146s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 146s -B: input BAM file(s) 146s 146s The input BAM file(s) must be sorted by coordinate. 146s With -B, records must be assigned to samples using BAM "reads groups" 146s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 146s must be consistent if repeated different files. Note that with -I, read 146s groups are unneeded and ignored. 146s 146s For both modes: 146s -M: path to a population map giving the list of samples 146s -O: output directory (default: none with -B; with -P same as the input 146s directory) 146s -t,--threads: number of threads to use (default: 1) 146s 146s SNP Model options: 146s --model: model to use to call variants and genotypes; one of 146s marukilow (default), marukihigh, or snp 146s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 146s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 146s 146s Paired-end options: 146s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 146s have the same insert length (implies --rm-unpaired-reads) 146s --rm-unpaired-reads: discard unpaired reads 146s --ignore-pe-reads: ignore paired-end reads even if present in the input 146s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 146s 146s Advanced options: 146s (De novo mode) 146s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 146s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 146s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 146s --write-alignments: save read alignments (heavy BAM files) 146s 146s (Reference-based mode) 146s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 146s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 146s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 146s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 146s 146s --details: write a heavier output 146s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 146s iterate over when building the graph of allele cooccurrences for 146s SNP phasing (default: 1,2) 146s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 146s genotypes during phasing 146s 146s kmer_filter 2.67 146s 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] 146s f: path to the input file if processing single-end seqeunces. 146s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 146s p: path to a directory of files (for single-end files only). 146s 1: specify the first in a pair of files to be processed together. 146s 2: specify the second in a pair of files to be processed together. 146s o: path to output the processed files. 146s y: output type, either 'fastq' or 'fasta' (default fastq). 146s D: capture discarded reads to a file. 146s h: display this help message. 146s 146s Filtering options: 146s --rare: turn on filtering based on rare k-mers. 146s --abundant: turn on filtering based on abundant k-mers. 146s --k-len : specify k-mer size (default 15). 146s 146s Advanced filtering options: 146s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 146s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 146s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 146s 146s Normalize data: 146s --normalize : normalize read depth according to k-mer coverage. 146s 146s Characterizing K-mers: 146s --write-k-freq: write kmers along with their frequency of occurrence and exit. 146s --k-dist: print k-mer frequency distribution and exit. 146s 146s Advanced input options: 146s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 146s 146s phasedstacks 2.67 146s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 146s b: Stacks batch ID. 146s P: path to the phased output files. 146s S: path to the Stacks output files. 146s t: input file type. Supported types: fastphase, and beagle. 146s p: number of processes to run in parallel sections of code. 146s M: path to the population map, a tab separated file describing which individuals belong in which population. 146s v: print program version. 146s h: display this help message. 146s --haplotypes: data were phased as RAD locus haplotypes. 146s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 146s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 146s 146s Filtering options: 146s --skip-zeros: do not include D' values of zero in the D' output. 146s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 146s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 146s 146s populations 2.67 146s Usage: 146s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 146s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 146s 146s -P,--in-path: path to a directory containing Stacks output files. 146s -V,--in-vcf: path to a standalone input VCF file. 146s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 146s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 146s -t,--threads: number of threads to run in parallel sections of code. 146s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 146s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 146s 146s Data Filtering: 146s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 146s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 146s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 146s -H,--filter-haplotype-wise: apply the above filters haplotype wise 146s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 146s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 146s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 146s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 146s --min-gt-depth [int]: specify a minimum number of reads to include a called SNP (otherwise marked as missing data). 146s 146s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 146s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 146s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 146s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 146s 146s Locus stats: 146s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 146s 146s Fstats: 146s --fstats: enable SNP and haplotype-based F statistics. 146s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 146s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 146s 146s Kernel-smoothing algorithm: 146s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 146s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 146s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 146s (Note: turning on smoothing implies --ordered-export.) 146s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 146s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 146s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 146s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 146s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 146s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 146s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 146s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 146s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 146s 146s File output options: 146s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 146s --fasta-loci: output locus consensus sequences in FASTA format. 146s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 146s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 146s --vcf-all: output all sites in Variant Call Format (VCF). 146s --genepop: output SNPs and haplotypes in GenePop format. 146s --structure: output results in Structure format. 146s --radpainter: output results in fineRADstructure/RADpainter format. 146s --plink: output genotypes in PLINK format. 146s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 146s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 146s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 146s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 146s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 146s --gtf: output locus positions in a GTF annotation file. 146s --no-hap-exports: omit haplotype outputs. 146s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 146s 146s Genetic map output options (population map must specify a genetic cross): 146s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 146s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 146s 146s Additional options: 146s -h,--help: display this help message. 146s -v,--version: print program version. 146s --verbose: turn on additional logging. 146s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 146s process_radtags 2.67 146s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 146s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 146s 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] 146s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 146s 146s -p,--in-path: path to a directory of files. 146s -P,--paired: files contained within the directory are paired. 146s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 146s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 146s -f: path to the input file if processing single-end sequences. 146s -1: first input file in a set of paired-end sequences. 146s -2: second input file in a set of paired-end sequences. 146s -o,--out-path: path to output the processed files. 146s --basename: specify the prefix of the output files when using -f or -1/-2. 146s 146s --threads: number of threads to run. 146s -c,--clean: clean data, remove any read with an uncalled base ('N'). 146s -q,--quality: discard reads with low quality (phred) scores. 146s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 146s -t,--truncate: truncate final read length to this value. 146s -D,--discards: capture discarded reads to a file. 146s 146s Barcode options: 146s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 146s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 146s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 146s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 146s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 146s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 146s --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). 146s 146s Restriction enzyme options: 146s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 146s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 146s Currently supported enzymes include: 146s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 146s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 146s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 146s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 146s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 146s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 146s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 146s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 146s 146s Protocol-specific options: 146s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 146s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 146s 146s Adapter options: 146s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 146s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 146s --adapter-mm : number of mismatches allowed in the adapter sequence. 146s 146s Input/Output options: 146s --in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 146s --out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 146s --retain-header: retain unmodified FASTQ headers in the output. 146s --merge: if no barcodes are specified, merge all input files into a single output file. 146s 146s Advanced options: 146s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 146s --disable-rad-check: disable checking if the RAD cut site is intact. 146s --force-poly-g-check: force a check for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 146s --disable-poly-g-check: disable checking for runs of poly-Gs (default: autodetect based on machine type in FASTQ header). 146s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 146s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 146s --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). 146s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 146s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 146s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 146s process_shortreads 2.67 146s 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] 146s f: path to the input file if processing single-end seqeunces. 146s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 146s p: path to a directory of single-end Illumina files. 146s 1: first input file in a set of paired-end sequences. 146s 2: second input file in a set of paired-end sequences. 146s P: specify that input is paired (for use with '-p'). 146s I: specify that the paired-end reads are interleaved in single files. 146s o: path to output the processed files. 146s y: output type, either 'fastq' or 'fasta' (default gzfastq). 146s b: a list of barcodes for this run. 146s c: clean data, remove any read with an uncalled base. 146s q: discard reads with low quality scores. 146s r: rescue barcodes. 146s t: truncate final read length to this value. 146s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 146s D: capture discarded reads to a file. 146s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 146s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 146s h: display this help message. 146s 146s Barcode options: 146s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 146s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 146s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 146s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 146s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 146s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 146s --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). 146s 146s Adapter options: 146s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 146s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 146s --adapter-mm : number of mismatches allowed in the adapter sequence. 146s 146s Output options: 146s --retain-header: retain unmodified FASTQ headers in the output. 146s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 146s 146s Advanced options: 146s --no-read-trimming: do not trim low quality reads, just discard them. 146s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 146s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 146s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 146s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 146s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 146s ref_map.pl 2.67 146s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 146s 146s Input/Output files: 146s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 146s --popmap: path to a population map file (format is " TAB ", one sample per line). 146s -s: spacer for file names: by default this is empty and the program looks for files 146s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 146s named 'SAMPLE_NAME.SPACER.bam'. 146s -o,--out-path: path to an output directory. 146s 146s General options: 146s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 146s -T: the number of threads/CPUs to use (default: 1). 146s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 146s that would be executed. 146s 146s SNP model options: 146s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 146s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 146s 146s Paired-end options: 146s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 146s the same insert length. 146s --ignore-pe-reads: ignore paired-end reads even if present in the input 146s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 146s 146s Population filtering options: 146s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 146s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 146s 146s Miscellaneous: 146s --time-components (for benchmarking) 146s sstacks 2.67 146s sstacks -P dir -M popmap [-t n_threads] 146s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads] 146s -P,--in-path: path to the directory containing Stacks files. 146s -M,--popmap: path to a population map file from which to take sample names. 146s -s,--sample: filename prefix from which to load sample loci. 146s -c,--catalog: path to the catalog. 146s -t,--threads: enable parallel execution with n_threads threads. 146s -o,--out-path: output path to write results. 146s -x: don't verify haplotype of matching locus. 146s 146s Gapped assembly options: 146s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 146s usage: 146s stacks-dist-extract logfile [section] 146s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 146s cat logfile | stacks-dist-extract [--pretty] [--section section] 146s 146s Export a paricular section of a Stacks log or distribs file. If you supply a 146s log path alone, stacks-dist-extract will print the available sections to 146s output. The log file can also be supplied via stdin. 146s 146s options: 146s -h, --help show this help message and exit 146s -p, --pretty Output data as a table with columns lined up. 146s -o path, --out-path path 146s Path to output file. 146s -s section, --section section 146s Name of section to output from the log file. 146s Usage: 146s stacks-gdb PROGRAM ARGUMENTS 146s 146s e.g. 146s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 146s 146s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 146s case of a crash it will print additional information, helping us in fixing the 146s crash. 146s 146s This utility requires GDB, the GNU Debugger, to be installed on the system where 146s Stacks is run. You can check whether this is the case by just typing: 146s 146s gdb --version 146s 146s at the command prompt. Note that you may need to load the corresponding module. 146s GDB is standard scientific software, but may not be installed on some systems. 146s For further information please contact the administrators of your system; 146s trying to install GDB without administrator priviledges is not recommended. 146s 146s For questions please contact us, e.g. at stacks-users@googlegroups.com 146s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 146s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 146s [--version] 146s 146s Extracts the coordinates of the RAD loci from the given BAM file into a 146s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 146s 'catalog.calls' files so that they include the genomic coordinates given in 146s the input BAM file. 146s 146s options: 146s -h, --help show this help message and exit 146s -P path, --in-path path 146s Path to a directory containing Stacks ouput files. 146s -B path, --bam-path path 146s Path to a SAM or BAM file containing alignment of de 146s novo catalog loci to a reference genome. 146s -O path, --out-path path 146s Path to write the integrated ouput files. 146s -q MIN_MAPQ, --min_mapq MIN_MAPQ 146s Minimum mapping quality as listed in the BAM file 146s (default 20). 146s -a MIN_ALNCOV, --min_alncov MIN_ALNCOV 146s Minimum fraction of the de novo catalog locus that 146s must participate in the alignment (default 0.6). 146s -p MIN_PCTID, --min_pctid MIN_PCTID 146s Minimum BLAST-style percent identity of the largest 146s alignment fragment for a de novo catalog locus 146s (default 0.6). 146s --verbose Provide verbose output. 146s --version show program's version number and exit 146s usage: 146s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 146s 146s Displays the read alignments of the given sample for the given locus, in text 146s format, to the standard output. Requires gstacks to have been run with the 146s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 146s tsv2bam 2.67 146s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 146s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 146s 146s -P,--in-dir: input directory. 146s -M,--popmap: population map. 146s -s,--sample: name of one sample. 146s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 146s -t: number of threads to use (default: 1). 146s 146s ustacks 2.67 146s ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads] 146s -f,--file: input file path. 146s -o,--out-path: output path to write results. 146s -M: Maximum distance (in nucleotides) allowed between stacks (default 2). 146s -m: Minimum number of reads to seed a new stack (default 3). 146s -N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 146s -t,--threads: enable parallel execution with num_threads threads. 146s -i,--in-type: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 146s -n,--name: a name for the sample (default: input file name minus the suffix). 146s -R: retain unused reads. 146s -H: disable calling haplotypes from secondary reads. 146s 146s Stack assembly options: 146s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 146s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 146s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 146s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 146s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 146s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 146s 146s Gapped assembly options: 146s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 146s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 146s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 146s 146s Model options: 146s --model-type: either 'snp' (default), 'bounded', or 'fixed' 146s For the SNP or Bounded SNP model: 146s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 146s For the Bounded SNP model: 146s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 146s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 146s For the Fixed model: 146s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 146s 146s h: display this help message. 146s autopkgtest [07:45:35]: test run-unit-test: -----------------------] 147s run-unit-test PASS (superficial) 147s autopkgtest [07:45:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 147s autopkgtest [07:45:36]: @@@@@@@@@@@@@@@@@@@@ summary 147s run-unit-test PASS (superficial) 160s nova [W] Using flock in prodstack6-ppc64el 160s flock: timeout while waiting to get lock 160s Creating nova instance adt-plucky-ppc64el-stacks-20241103-074309-juju-7f2275-prod-proposed-migration-environment-15-a4dcec1c-5be6-4ab6-b897-3a199f6b76d2 from image adt/ubuntu-plucky-ppc64el-server-20241103.img (UUID 8938751d-c60c-4749-8c34-7df179962ea5)...