0s autopkgtest [15:50:00]: starting date and time: 2024-03-23 15:50:00+0000 0s autopkgtest [15:50:00]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:50:00]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tt7eugfn/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:samtools,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=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 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@bos01-ppc64el-14.secgroup --name adt-noble-ppc64el-stacks-20240323-155000-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://us.ports.ubuntu.com/ubuntu-ports/ 102s autopkgtest [15:51:42]: testbed dpkg architecture: ppc64el 103s autopkgtest [15:51:43]: testbed apt version: 2.7.12 103s autopkgtest [15:51:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 104s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 104s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 104s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 104s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 104s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 104s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 104s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 104s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 104s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 104s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 104s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 104s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 108s Fetched 9623 kB in 2s (4303 kB/s) 108s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Calculating upgrade... 111s The following packages will be REMOVED: 111s libssl3 111s The following NEW packages will be installed: 111s libssl3t64 111s The following packages have been kept back: 111s curl 111s The following packages will be upgraded: 111s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales openssl 111s python3-markupsafe 111s 8 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 111s Need to get 12.1 MB of archives. 111s After this operation, 10.2 kB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 111s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 111s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 111s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 112s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 112s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 112s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 112s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 112s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB] 112s Preconfiguring packages ... 112s Fetched 12.1 MB in 1s (10.1 MB/s) 112s (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 ... 70157 files and directories currently installed.) 112s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 112s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 113s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 113s (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 ... 70157 files and directories currently installed.) 113s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 113s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 113s Setting up libc-bin (2.39-0ubuntu6) ... 113s (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 ... 70157 files and directories currently installed.) 113s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 113s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 113s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 113s wget depends on libssl3 (>= 3.0.0). 113s tnftp depends on libssl3 (>= 3.0.0). 113s tcpdump depends on libssl3 (>= 3.0.0). 113s systemd-resolved depends on libssl3 (>= 3.0.0). 113s systemd depends on libssl3 (>= 3.0.0). 113s sudo depends on libssl3 (>= 3.0.0). 113s rsync depends on libssl3 (>= 3.0.0). 113s python3-cryptography depends on libssl3 (>= 3.0.0). 113s openssh-server depends on libssl3 (>= 3.0.10). 113s openssh-client depends on libssl3 (>= 3.0.10). 113s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 113s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 113s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 113s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 113s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 113s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 113s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 113s libnvme1 depends on libssl3 (>= 3.0.0). 113s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 113s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 113s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 113s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 113s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 113s kmod depends on libssl3 (>= 3.0.0). 113s dhcpcd-base depends on libssl3 (>= 3.0.0). 113s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 113s 113s (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 ... 70157 files and directories currently installed.) 113s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 113s Selecting previously unselected package libssl3t64:ppc64el. 113s (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 ... 70146 files and directories currently installed.) 113s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 113s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 114s Preparing to unpack .../1-libbsd0_0.12.1-1_ppc64el.deb ... 114s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 114s Preparing to unpack .../2-locales_2.39-0ubuntu6_all.deb ... 114s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 114s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 114s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 114s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 114s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 114s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 114s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 114s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 114s Setting up cloud-init (24.1.2-0ubuntu1) ... 116s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 116s Setting up locales (2.39-0ubuntu6) ... 116s Generating locales (this might take a while)... 117s en_US.UTF-8... done 117s Generation complete. 117s Setting up python3-markupsafe (2.1.5-1build1) ... 117s Setting up openssl (3.0.13-0ubuntu2) ... 117s Setting up libbsd0:ppc64el (0.12.1-1) ... 117s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 118s Processing triggers for man-db (2.12.0-3) ... 119s Processing triggers for libc-bin (2.39-0ubuntu6) ... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 120s sh: Attempting to set up Debian/Ubuntu apt sources automatically 120s sh: Distribution appears to be Ubuntu 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s eatmydata is already the newest version (131-1). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s dbus is already the newest version (1.14.10-4ubuntu1). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s rng-tools-debian is already the newest version (2.4). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s The following packages will be REMOVED: 122s cloud-init* python3-configobj* python3-debconf* 122s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 122s After this operation, 3256 kB disk space will be freed. 122s (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.) 122s Removing cloud-init (24.1.2-0ubuntu1) ... 122s Removing python3-configobj (5.0.8-3) ... 122s Removing python3-debconf (1.5.86) ... 122s Processing triggers for man-db (2.12.0-3) ... 123s (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.) 123s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 123s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 123s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 123s invoke-rc.d: policy-rc.d denied execution of try-restart. 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s linux-generic is already the newest version (6.8.0-11.11+1). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 124s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 127s Reading package lists... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Calculating upgrade... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s autopkgtest [15:52:08]: rebooting testbed after setup commands that affected boot 285s autopkgtest [15:54:45]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 289s autopkgtest [15:54:49]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 290s Get:1 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (dsc) [2041 B] 290s Get:2 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (tar) [339 kB] 290s Get:3 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (diff) [12.1 kB] 291s gpgv: Signature made Tue Jan 23 12:37:41 2024 UTC 291s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 291s gpgv: Can't check signature: No public key 291s dpkg-source: warning: cannot verify inline signature for ./stacks_2.66+dfsg-1.dsc: no acceptable signature found 291s autopkgtest [15:54:51]: testing package stacks version 2.66+dfsg-1 291s autopkgtest [15:54:51]: build not needed 292s autopkgtest [15:54:52]: test run-unit-test: preparing testbed 308s Reading package lists... 309s Building dependency tree... 309s Reading state information... 309s Starting pkgProblemResolver with broken count: 0 309s Starting 2 pkgProblemResolver with broken count: 0 309s Done 309s The following additional packages will be installed: 309s libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 samtools stacks 309s Suggested packages: 309s libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl cwltool 309s gdb 309s Recommended packages: 309s libspreadsheet-writeexcel-perl littler 309s The following NEW packages will be installed: 309s autopkgtest-satdep libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 309s samtools stacks 309s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 309s Need to get 3414 kB/3415 kB of archives. 309s After this operation, 11.3 MB of additional disk space will be used. 309s Get:1 /tmp/autopkgtest.Lgr67P/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 309s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libdbi-perl ppc64el 1.643-4build1 [729 kB] 310s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 310s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 310s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 310s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 310s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el samtools ppc64el 1.19.2-1 [669 kB] 310s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el stacks ppc64el 2.66+dfsg-1 [1131 kB] 310s Fetched 3414 kB in 1s (4466 kB/s) 310s Selecting previously unselected package libdbi-perl:ppc64el. 310s (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.) 310s Preparing to unpack .../0-libdbi-perl_1.643-4build1_ppc64el.deb ... 310s Unpacking libdbi-perl:ppc64el (1.643-4build1) ... 310s Selecting previously unselected package libdeflate0:ppc64el. 310s Preparing to unpack .../1-libdeflate0_1.19-1_ppc64el.deb ... 310s Unpacking libdeflate0:ppc64el (1.19-1) ... 310s Selecting previously unselected package libgomp1:ppc64el. 310s Preparing to unpack .../2-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 310s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 310s Selecting previously unselected package libhtscodecs2:ppc64el. 310s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_ppc64el.deb ... 310s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 310s Selecting previously unselected package libhts3:ppc64el. 310s Preparing to unpack .../4-libhts3_1.18+ds-1_ppc64el.deb ... 310s Unpacking libhts3:ppc64el (1.18+ds-1) ... 310s Selecting previously unselected package samtools. 310s Preparing to unpack .../5-samtools_1.19.2-1_ppc64el.deb ... 310s Unpacking samtools (1.19.2-1) ... 310s Selecting previously unselected package stacks. 310s Preparing to unpack .../6-stacks_2.66+dfsg-1_ppc64el.deb ... 310s Unpacking stacks (2.66+dfsg-1) ... 310s Selecting previously unselected package autopkgtest-satdep. 310s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 310s Unpacking autopkgtest-satdep (0) ... 310s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 310s Setting up libdeflate0:ppc64el (1.19-1) ... 310s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 310s Setting up libdbi-perl:ppc64el (1.643-4build1) ... 310s Setting up libhts3:ppc64el (1.18+ds-1) ... 310s Setting up samtools (1.19.2-1) ... 310s Setting up stacks (2.66+dfsg-1) ... 310s Setting up autopkgtest-satdep (0) ... 310s Processing triggers for man-db (2.12.0-3) ... 311s Processing triggers for libc-bin (2.39-0ubuntu6) ... 313s (Reading database ... 70029 files and directories currently installed.) 313s Removing autopkgtest-satdep (0) ... 314s autopkgtest [15:55:14]: test run-unit-test: [----------------------- 314s Stacks - a pipeline for building loci from short-read sequences 314s v2.66+dfsg http://creskolab.uoregon.edu/stacks/ 314s 314s This is the Stacks wrapper script for Debian. Usage: 314s stacks 314s 314s Programs available are: 314s clone_filter ref_map 314s cstacks sstacks 314s denovo_map stacks-dist-extract 314s gstacks stacks-gdb 314s kmer_filter stacks-integrate-alignments 314s phasedstacks stacks-samtools-tview 314s populations tsv2bam 314s process_radtags ustacks 314s process_shortreads 314s 314s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 314s 314s clone_filter 2.66 314s 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] 314s f: path to the input file if processing single-end sequences. 314s p: path to a directory of files. 314s P: files contained within directory specified by '-p' are paired. 314s 1: first input file in a set of paired-end sequences. 314s 2: second input file in a set of paired-end sequences. 314s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 314s o: path to output the processed files. 314s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 314s D: capture discarded reads to a file. 314s h: display this help message. 314s --oligo-len-1 len: length of the single-end oligo sequence in data set. 314s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 314s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 314s 314s Oligo sequence options: 314s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 314s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 314s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 314s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 314s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 314s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 314s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 314s --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). 314s 314s cstacks 2.66 314s cstacks -P in_dir -M popmap [-n num_mismatches] [-p num_threads] 314s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-p num_threads] 314s 314s -P,--in-path: path to the directory containing Stacks files. 314s -M,--popmap: path to a population map file. 314s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 314s -p,--threads: enable parallel execution with num_threads threads. 314s -s: sample prefix from which to load loci into the catalog. 314s -o,--outpath: output path to write results. 314s -c,--catalog : add to an existing catalog. 314s 314s Gapped assembly options: 314s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 314s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 314s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 314s 314s Advanced options: 314s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 314s --report-mmatches: report query loci that match more than one catalog locus. 314s denovo_map.pl 2.66 314s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 314s 314s Input/Output files: 314s --samples: path to the directory containing the reads files for each sample. 314s --popmap: path to a population map file (format is " TAB ", one sample per line). 314s -o,--out-path: path to an output directory. 314s 314s General options: 314s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 314s -T, --threads: the number of threads/CPUs to use (default: 1). 314s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 314s --resume: resume executing the pipeline from a previous run. 314s 314s Stack assembly options: 314s -M: number of mismatches allowed between stacks within individuals (for ustacks). 314s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 314s 314s SNP model options: 314s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 314s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 314s 314s Paired-end options: 314s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 314s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 314s the same insert length. 314s 314s Population filtering options: 314s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 314s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 314s 314s For large datasets: 314s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 314s 314s Miscellaneous: 314s --time-components (for benchmarking) 314s gstacks 2.66 314s 314s De novo mode: 314s gstacks -P stacks_dir -M popmap 314s 314s -P: input directory containing '*.matches.bam' files created by the 314s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 314s 314s Reference-based mode: 314s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 314s gstacks -B bam_file [-B ...] -O out_dir 314s 314s -I: input directory containing BAM files 314s -S: with -I/-M, suffix to use to build BAM file names: by default this 314s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 314s -B: input BAM file(s) 314s 314s The input BAM file(s) must be sorted by coordinate. 314s With -B, records must be assigned to samples using BAM "reads groups" 314s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 314s must be consistent if repeated different files. Note that with -I, read 314s groups are unneeded and ignored. 314s 314s For both modes: 314s -M: path to a population map giving the list of samples 314s -O: output directory (default: none with -B; with -P same as the input 314s directory) 314s -t,--threads: number of threads to use (default: 1) 314s 314s SNP Model options: 314s --model: model to use to call variants and genotypes; one of 314s marukilow (default), marukihigh, or snp 314s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 314s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 314s 314s Paired-end options: 314s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 314s have the same insert length (implies --rm-unpaired-reads) 314s --rm-unpaired-reads: discard unpaired reads 314s --ignore-pe-reads: ignore paired-end reads even if present in the input 314s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 314s 314s Advanced options: 314s (De novo mode) 314s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 314s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 314s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 314s --write-alignments: save read alignments (heavy BAM files) 314s 314s (Reference-based mode) 314s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 314s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 314s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 314s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 314s 314s --details: write a heavier output 314s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 314s iterate over when building the graph of allele cooccurrences for 314s SNP phasing (default: 1,2) 314s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 314s genotypes during phasing 314s 314s kmer_filter 2.66 314s 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] 314s f: path to the input file if processing single-end seqeunces. 314s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 314s p: path to a directory of files (for single-end files only). 314s 1: specify the first in a pair of files to be processed together. 314s 2: specify the second in a pair of files to be processed together. 314s o: path to output the processed files. 314s y: output type, either 'fastq' or 'fasta' (default fastq). 314s D: capture discarded reads to a file. 314s h: display this help message. 314s 314s Filtering options: 314s --rare: turn on filtering based on rare k-mers. 314s --abundant: turn on filtering based on abundant k-mers. 314s --k-len : specify k-mer size (default 15). 314s 314s Advanced filtering options: 314s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 314s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 314s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 314s 314s Normalize data: 314s --normalize : normalize read depth according to k-mer coverage. 314s 314s Characterizing K-mers: 314s --write-k-freq: write kmers along with their frequency of occurrence and exit. 314s --k-dist: print k-mer frequency distribution and exit. 314s 314s Advanced input options: 314s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 314s 314s phasedstacks 2.66 314s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 314s b: Stacks batch ID. 314s P: path to the phased output files. 314s S: path to the Stacks output files. 314s t: input file type. Supported types: fastphase, and beagle. 314s p: number of processes to run in parallel sections of code. 314s M: path to the population map, a tab separated file describing which individuals belong in which population. 314s v: print program version. 314s h: display this help message. 314s --haplotypes: data were phased as RAD locus haplotypes. 314s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 314s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 314s 314s Filtering options: 314s --skip-zeros: do not include D' values of zero in the D' output. 314s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 314s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 314s 314s populations 2.66 314s Usage: 314s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 314s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 314s 314s -P,--in-path: path to a directory containing Stacks output files. 314s -V,--in-vcf: path to a standalone input VCF file. 314s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 314s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 314s -t,--threads: number of threads to run in parallel sections of code. 314s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 314s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 314s 314s Data Filtering: 314s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 314s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 314s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 314s -H,--filter-haplotype-wise: apply the above filters haplotype wise 314s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 314s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 314s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 314s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 314s 314s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 314s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 314s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 314s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 314s 314s Locus stats: 314s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 314s 314s Fstats: 314s --fstats: enable SNP and haplotype-based F statistics. 314s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 314s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 314s 314s Kernel-smoothing algorithm: 314s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 314s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 314s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 314s (Note: turning on smoothing implies --ordered-export.) 314s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 314s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 314s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 314s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 314s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 314s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 314s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 314s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 314s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 314s 314s File output options: 314s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 314s --fasta-loci: output locus consensus sequences in FASTA format. 314s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 314s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 314s --vcf-all: output all sites in Variant Call Format (VCF). 314s --genepop: output SNPs and haplotypes in GenePop format. 314s --structure: output results in Structure format. 314s --radpainter: output results in fineRADstructure/RADpainter format. 314s --plink: output genotypes in PLINK format. 314s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 314s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 314s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 314s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 314s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 314s --gtf: output locus positions in a GTF annotation file. 314s --no-hap-exports: omit haplotype outputs. 314s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 314s 314s Genetic map output options (population map must specify a genetic cross): 314s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 314s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 314s 314s Additional options: 314s -h,--help: display this help message. 314s -v,--version: print program version. 314s --verbose: turn on additional logging. 314s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 314s process_radtags 2.66 314s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 314s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 314s 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] 314s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 314s 314s -p,--in-path: path to a directory of files. 314s -P,--paired: files contained within the directory are paired. 314s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 314s -i,--in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 314s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 314s -o,--out-path: path to output the processed files. 314s -f: path to the input file if processing single-end sequences. 314s -1: first input file in a set of paired-end sequences. 314s -2: second input file in a set of paired-end sequences. 314s --threads: number of threads to run. 314s -c,--clean: clean data, remove any read with an uncalled base ('N'). 314s -q,--quality: discard reads with low quality (phred) scores. 314s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 314s -t,--truncate: truncate final read length to this value. 314s -D,--discards: capture discarded reads to a file. 314s -y,--out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 314s 314s Barcode options: 314s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 314s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 314s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 314s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 314s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 314s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 314s --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). 314s 314s Restriction enzyme options: 314s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 314s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 314s Currently supported enzymes include: 314s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 314s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 314s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 314s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 314s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 314s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 314s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 314s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 314s 314s Protocol-specific options: 314s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 314s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 314s 314s Adapter options: 314s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 314s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 314s --adapter-mm : number of mismatches allowed in the adapter sequence. 314s 314s Output options: 314s --retain-header: retain unmodified FASTQ headers in the output. 314s --merge: if no barcodes are specified, merge all input files into a single output file. 314s 314s Advanced options: 314s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 314s --disable-rad-check: disable checking if the RAD cut site is intact. 314s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 314s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 314s --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). 314s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 314s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 314s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 314s process_shortreads 2.66 314s 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] 314s f: path to the input file if processing single-end seqeunces. 314s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 314s p: path to a directory of single-end Illumina files. 314s 1: first input file in a set of paired-end sequences. 314s 2: second input file in a set of paired-end sequences. 314s P: specify that input is paired (for use with '-p'). 314s I: specify that the paired-end reads are interleaved in single files. 314s o: path to output the processed files. 314s y: output type, either 'fastq' or 'fasta' (default gzfastq). 314s b: a list of barcodes for this run. 314s c: clean data, remove any read with an uncalled base. 314s q: discard reads with low quality scores. 314s r: rescue barcodes. 314s t: truncate final read length to this value. 314s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 314s D: capture discarded reads to a file. 314s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 314s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 314s h: display this help message. 314s 314s Barcode options: 314s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 314s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 314s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 314s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 314s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 314s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 314s --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). 314s 314s Adapter options: 314s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 314s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 314s --adapter-mm : number of mismatches allowed in the adapter sequence. 314s 314s Output options: 314s --retain-header: retain unmodified FASTQ headers in the output. 314s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 314s 314s Advanced options: 314s --no-read-trimming: do not trim low quality reads, just discard them. 314s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 314s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 314s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 314s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 314s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 314s ref_map.pl 2.66 314s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 314s 314s Input/Output files: 314s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 314s --popmap: path to a population map file (format is " TAB ", one sample per line). 314s -s: spacer for file names: by default this is empty and the program looks for files 314s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 314s named 'SAMPLE_NAME.SPACER.bam'. 314s -o,--out-path: path to an output directory. 314s 314s General options: 314s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 314s -T: the number of threads/CPUs to use (default: 1). 314s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 314s that would be executed. 314s 314s SNP model options: 314s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 314s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 314s 314s Paired-end options: 314s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 314s the same insert length. 314s --ignore-pe-reads: ignore paired-end reads even if present in the input 314s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 314s 314s Population filtering options: 314s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 314s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 314s 314s Miscellaneous: 314s --time-components (for benchmarking) 314s sstacks 2.66 314s sstacks -P dir -M popmap [-p n_threads] 314s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] 314s -P,--in-path: path to the directory containing Stacks files. 314s -M,--popmap: path to a population map file from which to take sample names. 314s -s,--sample: filename prefix from which to load sample loci. 314s -c,--catalog: path to the catalog. 314s -p,--threads: enable parallel execution with n_threads threads. 314s -o,--out-path: output path to write results. 314s -x: don't verify haplotype of matching locus. 314s 314s Gapped assembly options: 314s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 314s usage: 314s stacks-dist-extract logfile [section] 314s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 314s cat logfile | stacks-dist-extract [--pretty] [--section section] 314s 314s Export a paricular section of a Stacks log or distribs file. If you supply a 314s log path alone, stacks-dist-extract will print the available sections to 314s output. The log file can also be supplied via stdin. 314s 314s options: 314s -h, --help show this help message and exit 314s -p, --pretty Output data as a table with columns lined up. 314s -o path, --out-path path 314s Path to output file. 314s -s section, --section section 314s Name of section to output from the log file. 314s Usage: 314s stacks-gdb PROGRAM ARGUMENTS 314s 314s e.g. 314s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 314s 314s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 314s case of a crash it will print additional information, helping us in fixing the 314s crash. 314s 314s This utility requires GDB, the GNU Debugger, to be installed on the system where 314s Stacks is run. You can check whether this is the case by just typing: 314s 314s gdb --version 314s 314s at the command prompt. Note that you may need to load the corresponding module. 314s GDB is standard scientific software, but may not be installed on some systems. 314s For further information please contact the administrators of your system; 314s trying to install GDB without administrator priviledges is not recommended. 314s 314s For questions please contact us, e.g. at stacks-users@googlegroups.com 314s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 314s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 314s [--version] 314s 314s Extracts the coordinates of the RAD loci from the given BAM file into a 314s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 314s 'catalog.calls' files so that they include the genomic coordinates given in 314s the input BAM file. 314s 314s options: 314s -h, --help show this help message and exit 314s -P path, --in-path path 314s Path to a directory containing Stacks ouput files. 314s -B path, --bam-path path 314s Path to a SAM or BAM file containing alignment of de 314s novo catalog loci to a reference genome. 314s -O path, --out-path path 314s Path to write the integrated ouput files. 314s -q MIN_MAPQ, --min_mapq MIN_MAPQ 314s Minimum mapping quality as listed in the BAM file 314s (default 20). 314s -a MIN_ALNCOV, --min_alncov MIN_ALNCOV 314s Minimum fraction of the de novo catalog locus that 314s must participate in the alignment (default 0.6). 314s -p MIN_PCTID, --min_pctid MIN_PCTID 314s Minimum BLAST-style percent identity of the largest 314s alignment fragment for a de novo catalog locus 314s (default 0.6). 314s --verbose Provide verbose output. 314s --version show program's version number and exit 314s usage: 314s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 314s 314s Displays the read alignments of the given sample for the given locus, in text 314s format, to the standard output. Requires gstacks to have been run with the 314s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 314s tsv2bam 2.66 314s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 314s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 314s 314s -P,--in-dir: input directory. 314s -M,--popmap: population map. 314s -s,--sample: name of one sample. 314s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 314s -t: number of threads to use (default: 1). 314s 314s ustacks 2.66 314s ustacks -f file_path -o path [-M max_dist] [-m min_cov] [-p num_threads] 314s f: input file path. 314s o: output path to write results. 314s M: Maximum distance (in nucleotides) allowed between stacks (default 2). 314s m: Minimum depth of coverage required to create a stack (default 3). 314s N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 314s p: enable parallel execution with num_threads threads. 314s t: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 314s --name: a name for the sample (default: input file name minus the suffix). 314s R: retain unused reads. 314s H: disable calling haplotypes from secondary reads. 314s 314s Stack assembly options: 314s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 314s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 314s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 314s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 314s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 314s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 314s 314s Gapped assembly options: 314s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 314s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 314s 314s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 314s Model options: 314s --model-type: either 'snp' (default), 'bounded', or 'fixed' 314s For the SNP or Bounded SNP model: 314s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 314s For the Bounded SNP model: 314s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 314s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 314s For the Fixed model: 314s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 314s 314s h: display this help message. 315s autopkgtest [15:55:15]: test run-unit-test: -----------------------] 315s run-unit-test PASS (superficial) 315s autopkgtest [15:55:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 315s autopkgtest [15:55:15]: @@@@@@@@@@@@@@@@@@@@ summary 315s run-unit-test PASS (superficial) 329s Creating nova instance adt-noble-ppc64el-stacks-20240323-155000-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...