0s autopkgtest [22:35:01]: starting date and time: 2024-03-25 22:35:01+0000 0s autopkgtest [22:35:01]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [22:35:01]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w9e_zgjm/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:stacks,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade stacks --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=stacks/2.66+dfsg-1build1 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-14.secgroup --name adt-noble-ppc64el-stacks-20240325-223501-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 252s autopkgtest [22:39:13]: testbed dpkg architecture: ppc64el 252s autopkgtest [22:39:13]: testbed apt version: 2.7.12 252s autopkgtest [22:39:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 253s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 254s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 254s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4039 kB] 255s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 255s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 255s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [700 kB] 255s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 255s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 255s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 255s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4232 kB] 256s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 256s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 256s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 259s Fetched 9723 kB in 3s (2946 kB/s) 259s Reading package lists... 262s Reading package lists... 262s Building dependency tree... 262s Reading state information... 262s Calculating upgrade... 263s The following packages will be REMOVED: 263s libssl3 263s The following NEW packages will be installed: 263s libssl3t64 263s The following packages have been kept back: 263s curl 263s The following packages will be upgraded: 263s openssl 263s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 263s Need to get 3151 kB of archives. 263s After this operation, 73.7 kB of additional disk space will be used. 263s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 263s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 264s Fetched 3151 kB in 1s (2869 kB/s) 264s (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 ... 70156 files and directories currently installed.) 264s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 264s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 264s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 264s wget depends on libssl3 (>= 3.0.0). 264s tnftp depends on libssl3 (>= 3.0.0). 264s tcpdump depends on libssl3 (>= 3.0.0). 264s systemd-resolved depends on libssl3 (>= 3.0.0). 264s systemd depends on libssl3 (>= 3.0.0). 264s sudo depends on libssl3 (>= 3.0.0). 264s rsync depends on libssl3 (>= 3.0.0). 264s python3-cryptography depends on libssl3 (>= 3.0.0). 264s openssh-server depends on libssl3 (>= 3.0.10). 264s openssh-client depends on libssl3 (>= 3.0.10). 264s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 264s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 264s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 264s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 264s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 264s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 264s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 264s libnvme1 depends on libssl3 (>= 3.0.0). 264s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 264s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 264s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 264s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 264s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 264s kmod depends on libssl3 (>= 3.0.0). 264s dhcpcd-base depends on libssl3 (>= 3.0.0). 264s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 264s 264s (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 ... 70156 files and directories currently installed.) 264s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 264s Selecting previously unselected package libssl3t64:ppc64el. 264s (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 ... 70145 files and directories currently installed.) 264s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 264s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 265s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 265s Setting up openssl (3.0.13-0ubuntu2) ... 265s Processing triggers for man-db (2.12.0-3) ... 265s Processing triggers for libc-bin (2.39-0ubuntu6) ... 265s Reading package lists... 266s Building dependency tree... 266s Reading state information... 266s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 266s sh: Attempting to set up Debian/Ubuntu apt sources automatically 266s sh: Distribution appears to be Ubuntu 267s Reading package lists... 268s Building dependency tree... 268s Reading state information... 268s eatmydata is already the newest version (131-1). 268s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 268s Reading package lists... 268s Building dependency tree... 268s Reading state information... 268s dbus is already the newest version (1.14.10-4ubuntu1). 268s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 268s Reading package lists... 268s Building dependency tree... 268s Reading state information... 269s rng-tools-debian is already the newest version (2.4). 269s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 269s The following packages will be REMOVED: 269s cloud-init* python3-configobj* python3-debconf* 269s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 269s After this operation, 3256 kB disk space will be freed. 269s (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 ... 70158 files and directories currently installed.) 269s Removing cloud-init (24.1.2-0ubuntu1) ... 270s Removing python3-configobj (5.0.8-3) ... 270s Removing python3-debconf (1.5.86) ... 270s Processing triggers for man-db (2.12.0-3) ... 271s (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 ... 69769 files and directories currently installed.) 271s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 271s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 271s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 271s invoke-rc.d: policy-rc.d denied execution of try-restart. 271s Reading package lists... 272s Building dependency tree... 272s Reading state information... 272s linux-generic is already the newest version (6.8.0-11.11+1). 272s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 272s Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 273s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 273s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 273s Get:4 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 275s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el Packages [1376 kB] 275s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [15.2 MB] 283s Fetched 36.6 MB in 9s (3997 kB/s) 284s Reading package lists... 284s Reading package lists... 284s Building dependency tree... 284s Reading state information... 284s Calculating upgrade... 284s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 284s Reading package lists... 284s Building dependency tree... 284s Reading state information... 285s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 285s autopkgtest [22:39:46]: rebooting testbed after setup commands that affected boot 447s autopkgtest [22:42:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 450s autopkgtest [22:42:31]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 452s Get:1 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (dsc) [2041 B] 452s Get:2 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (tar) [339 kB] 452s Get:3 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (diff) [12.1 kB] 452s gpgv: Signature made Tue Jan 23 12:37:41 2024 UTC 452s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 452s gpgv: Can't check signature: No public key 452s dpkg-source: warning: cannot verify inline signature for ./stacks_2.66+dfsg-1.dsc: no acceptable signature found 453s autopkgtest [22:42:34]: testing package stacks version 2.66+dfsg-1 453s autopkgtest [22:42:34]: build not needed 453s autopkgtest [22:42:34]: test run-unit-test: preparing testbed 455s Reading package lists... 456s Building dependency tree... 456s Reading state information... 456s Starting pkgProblemResolver with broken count: 0 456s Starting 2 pkgProblemResolver with broken count: 0 456s Done 457s The following additional packages will be installed: 457s libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 samtools stacks 457s Suggested packages: 457s libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl cwltool 457s gdb 457s Recommended packages: 457s libspreadsheet-writeexcel-perl littler 457s The following NEW packages will be installed: 457s autopkgtest-satdep libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 457s samtools stacks 457s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 457s Need to get 3414 kB/3415 kB of archives. 457s After this operation, 11.3 MB of additional disk space will be used. 457s Get:1 /tmp/autopkgtest.W3itu5/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 457s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdbi-perl ppc64el 1.643-4build1 [729 kB] 458s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 458s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 458s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 458s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 458s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 458s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el stacks ppc64el 2.66+dfsg-1 [1131 kB] 459s Fetched 3414 kB in 2s (2164 kB/s) 459s Selecting previously unselected package libdbi-perl:ppc64el. 459s (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 ... 69714 files and directories currently installed.) 459s Preparing to unpack .../0-libdbi-perl_1.643-4build1_ppc64el.deb ... 459s Unpacking libdbi-perl:ppc64el (1.643-4build1) ... 459s Selecting previously unselected package libdeflate0:ppc64el. 459s Preparing to unpack .../1-libdeflate0_1.19-1_ppc64el.deb ... 459s Unpacking libdeflate0:ppc64el (1.19-1) ... 459s Selecting previously unselected package libgomp1:ppc64el. 459s Preparing to unpack .../2-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 459s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 459s Selecting previously unselected package libhtscodecs2:ppc64el. 459s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 459s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 459s Selecting previously unselected package libhts3:ppc64el. 459s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 459s Unpacking libhts3:ppc64el (1.18+ds-1) ... 459s Selecting previously unselected package samtools. 459s Preparing to unpack .../5-samtools_1.19.2-1_ppc64el.deb ... 459s Unpacking samtools (1.19.2-1) ... 459s Selecting previously unselected package stacks. 459s Preparing to unpack .../6-stacks_2.66+dfsg-1_ppc64el.deb ... 459s Unpacking stacks (2.66+dfsg-1) ... 459s Selecting previously unselected package autopkgtest-satdep. 459s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 459s Unpacking autopkgtest-satdep (0) ... 459s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 459s Setting up libdeflate0:ppc64el (1.19-1) ... 459s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 459s Setting up libdbi-perl:ppc64el (1.643-4build1) ... 459s Setting up libhts3:ppc64el (1.18+ds-1) ... 459s Setting up samtools (1.19.2-1) ... 459s Setting up stacks (2.66+dfsg-1) ... 459s Setting up autopkgtest-satdep (0) ... 459s Processing triggers for man-db (2.12.0-3) ... 460s Processing triggers for libc-bin (2.39-0ubuntu6) ... 463s (Reading database ... 70029 files and directories currently installed.) 463s Removing autopkgtest-satdep (0) ... 464s autopkgtest [22:42:45]: test run-unit-test: [----------------------- 464s Stacks - a pipeline for building loci from short-read sequences 464s v2.66+dfsg http://creskolab.uoregon.edu/stacks/ 464s 464s This is the Stacks wrapper script for Debian. Usage: 464s stacks 464s 464s Programs available are: 464s clone_filter ref_map 464s cstacks sstacks 464s denovo_map stacks-dist-extract 464s gstacks stacks-gdb 464s kmer_filter stacks-integrate-alignments 464s phasedstacks stacks-samtools-tview 464s populations tsv2bam 464s process_radtags ustacks 464s process_shortreads 464s 464s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 464s 464s clone_filter 2.66 464s 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] 464s f: path to the input file if processing single-end sequences. 464s p: path to a directory of files. 464s P: files contained within directory specified by '-p' are paired. 464s 1: first input file in a set of paired-end sequences. 464s 2: second input file in a set of paired-end sequences. 464s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 464s o: path to output the processed files. 464s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 464s D: capture discarded reads to a file. 464s h: display this help message. 464s --oligo-len-1 len: length of the single-end oligo sequence in data set. 464s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 464s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 464s 464s Oligo sequence options: 464s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 464s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 464s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 464s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 464s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 464s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 464s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 464s --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). 464s 464s cstacks 2.66 464s cstacks -P in_dir -M popmap [-n num_mismatches] [-p num_threads] 464s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-p num_threads] 464s 464s -P,--in-path: path to the directory containing Stacks files. 464s -M,--popmap: path to a population map file. 464s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 464s -p,--threads: enable parallel execution with num_threads threads. 464s -s: sample prefix from which to load loci into the catalog. 464s -o,--outpath: output path to write results. 464s -c,--catalog : add to an existing catalog. 464s 464s Gapped assembly options: 464s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 464s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 464s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 464s 464s Advanced options: 464s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 464s --report-mmatches: report query loci that match more than one catalog locus. 464s denovo_map.pl 2.66 464s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 464s 464s Input/Output files: 464s --samples: path to the directory containing the reads files for each sample. 464s --popmap: path to a population map file (format is " TAB ", one sample per line). 464s -o,--out-path: path to an output directory. 464s 464s General options: 464s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 464s -T, --threads: the number of threads/CPUs to use (default: 1). 464s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 464s --resume: resume executing the pipeline from a previous run. 464s 464s Stack assembly options: 464s -M: number of mismatches allowed between stacks within individuals (for ustacks). 464s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 464s 464s SNP model options: 464s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 464s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 464s 464s Paired-end options: 464s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 464s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 464s the same insert length. 464s 464s Population filtering options: 464s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 464s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 464s 464s For large datasets: 464s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 464s 464s Miscellaneous: 464s --time-components (for benchmarking) 464s gstacks 2.66 464s 464s De novo mode: 464s gstacks -P stacks_dir -M popmap 464s 464s -P: input directory containing '*.matches.bam' files created by the 464s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 464s 464s Reference-based mode: 464s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 464s gstacks -B bam_file [-B ...] -O out_dir 464s 464s -I: input directory containing BAM files 464s -S: with -I/-M, suffix to use to build BAM file names: by default this 464s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 464s -B: input BAM file(s) 464s 464s The input BAM file(s) must be sorted by coordinate. 464s With -B, records must be assigned to samples using BAM "reads groups" 464s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 464s must be consistent if repeated different files. Note that with -I, read 464s groups are unneeded and ignored. 464s 464s For both modes: 464s -M: path to a population map giving the list of samples 464s -O: output directory (default: none with -B; with -P same as the input 464s directory) 464s -t,--threads: number of threads to use (default: 1) 464s 464s SNP Model options: 464s --model: model to use to call variants and genotypes; one of 464s marukilow (default), marukihigh, or snp 464s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 464s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 464s 464s Paired-end options: 464s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 464s have the same insert length (implies --rm-unpaired-reads) 464s --rm-unpaired-reads: discard unpaired reads 464s --ignore-pe-reads: ignore paired-end reads even if present in the input 464s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 464s 464s Advanced options: 464s (De novo mode) 464s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 464s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 464s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 464s --write-alignments: save read alignments (heavy BAM files) 464s 464s (Reference-based mode) 464s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 464s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 464s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 464s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 464s 464s --details: write a heavier output 464s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 464s iterate over when building the graph of allele cooccurrences for 464s SNP phasing (default: 1,2) 464s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 464s genotypes during phasing 464s 464s kmer_filter 2.66 464s 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] 464s f: path to the input file if processing single-end seqeunces. 464s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 464s p: path to a directory of files (for single-end files only). 464s 1: specify the first in a pair of files to be processed together. 464s 2: specify the second in a pair of files to be processed together. 464s o: path to output the processed files. 464s y: output type, either 'fastq' or 'fasta' (default fastq). 464s D: capture discarded reads to a file. 464s h: display this help message. 464s 464s Filtering options: 464s --rare: turn on filtering based on rare k-mers. 464s --abundant: turn on filtering based on abundant k-mers. 464s --k-len : specify k-mer size (default 15). 464s 464s Advanced filtering options: 464s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 464s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 464s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 464s 464s Normalize data: 464s --normalize : normalize read depth according to k-mer coverage. 464s 464s Characterizing K-mers: 464s --write-k-freq: write kmers along with their frequency of occurrence and exit. 464s --k-dist: print k-mer frequency distribution and exit. 464s 464s Advanced input options: 464s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 464s 464s phasedstacks 2.66 464s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 464s b: Stacks batch ID. 464s P: path to the phased output files. 464s S: path to the Stacks output files. 464s t: input file type. Supported types: fastphase, and beagle. 464s p: number of processes to run in parallel sections of code. 464s M: path to the population map, a tab separated file describing which individuals belong in which population. 464s v: print program version. 464s h: display this help message. 464s --haplotypes: data were phased as RAD locus haplotypes. 464s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 464s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 464s 464s Filtering options: 464s --skip-zeros: do not include D' values of zero in the D' output. 464s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 464s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 464s 464s populations 2.66 464s Usage: 464s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 464s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 464s 464s -P,--in-path: path to a directory containing Stacks output files. 464s -V,--in-vcf: path to a standalone input VCF file. 464s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 464s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 464s -t,--threads: number of threads to run in parallel sections of code. 464s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 464s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 464s 464s Data Filtering: 464s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 464s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 464s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 464s -H,--filter-haplotype-wise: apply the above filters haplotype wise 464s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 464s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 464s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 464s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 464s 464s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 464s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 464s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 464s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 464s 464s Locus stats: 464s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 464s 464s Fstats: 464s --fstats: enable SNP and haplotype-based F statistics. 464s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 464s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 464s 464s Kernel-smoothing algorithm: 464s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 464s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 464s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 464s (Note: turning on smoothing implies --ordered-export.) 464s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 464s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 464s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 464s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 464s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 464s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 464s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 464s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 464s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 464s 464s File output options: 464s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 464s --fasta-loci: output locus consensus sequences in FASTA format. 464s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 464s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 464s --vcf-all: output all sites in Variant Call Format (VCF). 464s --genepop: output SNPs and haplotypes in GenePop format. 464s --structure: output results in Structure format. 464s --radpainter: output results in fineRADstructure/RADpainter format. 464s --plink: output genotypes in PLINK format. 464s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 464s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 464s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 464s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 464s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 464s --gtf: output locus positions in a GTF annotation file. 464s --no-hap-exports: omit haplotype outputs. 464s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 464s 464s Genetic map output options (population map must specify a genetic cross): 464s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 464s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 464s 464s Additional options: 464s -h,--help: display this help message. 464s -v,--version: print program version. 464s --verbose: turn on additional logging. 464s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 464s process_radtags 2.66 464s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 464s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 464s 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] 464s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 464s 464s -p,--in-path: path to a directory of files. 464s -P,--paired: files contained within the directory are paired. 464s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 464s -i,--in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 464s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 464s -o,--out-path: path to output the processed files. 464s -f: path to the input file if processing single-end sequences. 464s -1: first input file in a set of paired-end sequences. 464s -2: second input file in a set of paired-end sequences. 464s --threads: number of threads to run. 464s -c,--clean: clean data, remove any read with an uncalled base ('N'). 464s -q,--quality: discard reads with low quality (phred) scores. 464s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 464s -t,--truncate: truncate final read length to this value. 464s -D,--discards: capture discarded reads to a file. 464s -y,--out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 464s 464s Barcode options: 464s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 464s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 464s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 464s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 464s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 464s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 464s --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). 464s 464s Restriction enzyme options: 464s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 464s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 464s Currently supported enzymes include: 464s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 464s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 464s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 464s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 464s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 464s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 464s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 464s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 464s 464s Protocol-specific options: 464s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 464s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 464s 464s Adapter options: 464s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 464s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 464s --adapter-mm : number of mismatches allowed in the adapter sequence. 464s 464s Output options: 464s --retain-header: retain unmodified FASTQ headers in the output. 464s --merge: if no barcodes are specified, merge all input files into a single output file. 464s 464s Advanced options: 464s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 464s --disable-rad-check: disable checking if the RAD cut site is intact. 464s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 464s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 464s --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). 464s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 464s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 464s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 464s process_shortreads 2.66 464s 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] 464s f: path to the input file if processing single-end seqeunces. 464s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 464s p: path to a directory of single-end Illumina files. 464s 1: first input file in a set of paired-end sequences. 464s 2: second input file in a set of paired-end sequences. 464s P: specify that input is paired (for use with '-p'). 464s I: specify that the paired-end reads are interleaved in single files. 464s o: path to output the processed files. 464s y: output type, either 'fastq' or 'fasta' (default gzfastq). 464s b: a list of barcodes for this run. 464s c: clean data, remove any read with an uncalled base. 464s q: discard reads with low quality scores. 464s r: rescue barcodes. 464s t: truncate final read length to this value. 464s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 464s D: capture discarded reads to a file. 464s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 464s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 464s h: display this help message. 464s 464s Barcode options: 464s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 464s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 464s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 464s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 464s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 464s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 464s --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). 464s 464s Adapter options: 464s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 464s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 464s --adapter-mm : number of mismatches allowed in the adapter sequence. 464s 464s Output options: 464s --retain-header: retain unmodified FASTQ headers in the output. 464s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 464s 464s Advanced options: 464s --no-read-trimming: do not trim low quality reads, just discard them. 464s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 464s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 464s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 464s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 464s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 464s ref_map.pl 2.66 464s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 464s 464s Input/Output files: 464s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 464s --popmap: path to a population map file (format is " TAB ", one sample per line). 464s -s: spacer for file names: by default this is empty and the program looks for files 464s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 464s named 'SAMPLE_NAME.SPACER.bam'. 464s -o,--out-path: path to an output directory. 464s 464s General options: 464s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 464s -T: the number of threads/CPUs to use (default: 1). 464s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 464s that would be executed. 464s 464s SNP model options: 464s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 464s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 464s 464s Paired-end options: 464s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 464s the same insert length. 464s --ignore-pe-reads: ignore paired-end reads even if present in the input 464s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 464s 464s Population filtering options: 464s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 464s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 464s 464s Miscellaneous: 464s --time-components (for benchmarking) 464s sstacks 2.66 464s sstacks -P dir -M popmap [-p n_threads] 464s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] 464s -P,--in-path: path to the directory containing Stacks files. 464s -M,--popmap: path to a population map file from which to take sample names. 464s -s,--sample: filename prefix from which to load sample loci. 464s -c,--catalog: path to the catalog. 464s -p,--threads: enable parallel execution with n_threads threads. 464s -o,--out-path: output path to write results. 464s -x: don't verify haplotype of matching locus. 464s 464s Gapped assembly options: 464s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 464s usage: 464s stacks-dist-extract logfile [section] 464s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 464s cat logfile | stacks-dist-extract [--pretty] [--section section] 464s 464s Export a paricular section of a Stacks log or distribs file. If you supply a 464s log path alone, stacks-dist-extract will print the available sections to 464s output. The log file can also be supplied via stdin. 464s 464s options: 464s -h, --help show this help message and exit 464s -p, --pretty Output data as a table with columns lined up. 464s -o path, --out-path path 464s Path to output file. 464s -s section, --section section 464s Name of section to output from the log file. 464s Usage: 464s stacks-gdb PROGRAM ARGUMENTS 464s 464s e.g. 464s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 464s 464s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 464s case of a crash it will print additional information, helping us in fixing the 464s crash. 464s 464s This utility requires GDB, the GNU Debugger, to be installed on the system where 464s Stacks is run. You can check whether this is the case by just typing: 464s 464s gdb --version 464s 464s at the command prompt. Note that you may need to load the corresponding module. 464s GDB is standard scientific software, but may not be installed on some systems. 464s For further information please contact the administrators of your system; 464s trying to install GDB without administrator priviledges is not recommended. 464s 464s For questions please contact us, e.g. at stacks-users@googlegroups.com 464s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 464s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 464s [--version] 464s 464s Extracts the coordinates of the RAD loci from the given BAM file into a 464s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 464s 'catalog.calls' files so that they include the genomic coordinates given in 464s the input BAM file. 464s 464s options: 464s -h, --help show this help message and exit 464s -P path, --in-path path 464s Path to a directory containing Stacks ouput files. 464s -B path, --bam-path path 464s Path to a SAM or BAM file containing alignment of de 464s novo catalog loci to a reference genome. 464s -O path, --out-path path 464s Path to write the integrated ouput files. 464s -q MIN_MAPQ, --min_mapq MIN_MAPQ 464s Minimum mapping quality as listed in the BAM file 464s (default 20). 464s -a MIN_ALNCOV, --min_alncov MIN_ALNCOV 464s Minimum fraction of the de novo catalog locus that 464s must participate in the alignment (default 0.6). 464s -p MIN_PCTID, --min_pctid MIN_PCTID 464s Minimum BLAST-style percent identity of the largest 464s alignment fragment for a de novo catalog locus 464s (default 0.6). 464s --verbose Provide verbose output. 464s --version show program's version number and exit 464s usage: 464s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 464s 464s Displays the read alignments of the given sample for the given locus, in text 464s format, to the standard output. Requires gstacks to have been run with the 464s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 464s tsv2bam 2.66 464s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 464s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 464s 464s -P,--in-dir: input directory. 464s -M,--popmap: population map. 464s -s,--sample: name of one sample. 464s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 464s -t: number of threads to use (default: 1). 464s 464s ustacks 2.66 464s ustacks -f file_path -o path [-M max_dist] [-m min_cov] [-p num_threads] 464s f: input file path. 464s o: output path to write results. 464s M: Maximum distance (in nucleotides) allowed between stacks (default 2). 464s m: Minimum depth of coverage required to create a stack (default 3). 464s N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 464s p: enable parallel execution with num_threads threads. 464s t: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 464s --name: a name for the sample (default: input file name minus the suffix). 464s R: retain unused reads. 464s H: disable calling haplotypes from secondary reads. 464s 464s Stack assembly options: 464s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 464s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 464s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 464s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 464s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 464s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 464s 464s Gapped assembly options: 464s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 464s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 464s 464s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 464s Model options: 464s --model-type: either 'snp' (default), 'bounded', or 'fixed' 464s For the SNP or Bounded SNP model: 464s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 464s For the Bounded SNP model: 464s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 464s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 464s For the Fixed model: 464s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 464s 464s h: display this help message. 464s autopkgtest [22:42:45]: test run-unit-test: -----------------------] 465s autopkgtest [22:42:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 465s run-unit-test PASS (superficial) 465s autopkgtest [22:42:46]: @@@@@@@@@@@@@@@@@@@@ summary 465s run-unit-test PASS (superficial) 492s Creating nova instance adt-noble-ppc64el-stacks-20240325-223501-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...