Diff of the two buildlogs: -- --- b1/build.log 2024-05-29 11:18:39.482331988 +0000 +++ b2/build.log 2024-05-29 11:24:03.016571936 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 28 23:06:22 -12 2024 -I: pbuilder-time-stamp: 1716980782 +I: Current time: Wed Jul 2 07:41:38 +14 2025 +I: pbuilder-time-stamp: 1751391698 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying snpeff_v5.1+.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1133945/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 1 17:41 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='5ff3f424d8e44231803bb79c9ebef5f4' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1133945' - PS1='# ' - PS2='> ' + INVOCATION_ID=5773d1f7a1294495a6fd51f850767e6b + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3099667 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.l3KxjNW4/pbuilderrc_A2NM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.l3KxjNW4/b1 --logfile b1/build.log snippy_4.6.0+dfsg-4.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.l3KxjNW4/pbuilderrc_b0nq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.l3KxjNW4/b2 --logfile b2/build.log snippy_4.6.0+dfsg-4.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 27 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1133945/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 29 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -581,7 +613,7 @@ Get: 438 http://deb.debian.org/debian unstable/main amd64 snp-sites amd64 2.5.1-2+b1 [14.5 kB] Get: 439 http://deb.debian.org/debian unstable/main amd64 snpeff all 5.2.b+dfsg-1 [7164 B] Get: 440 http://deb.debian.org/debian unstable/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] -Fetched 378 MB in 18s (21.5 MB/s) +Fetched 378 MB in 13s (29.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19716 files and directories currently installed.) @@ -2001,8 +2033,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed May 29 11:10:31 UTC 2024. -Universal Time is now: Wed May 29 11:10:31 UTC 2024. +Local time is now: Tue Jul 1 17:43:44 UTC 2025. +Universal Time is now: Tue Jul 1 17:43:44 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -2552,7 +2584,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snippy_4.6.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snippy_4.6.0+dfsg-4_source.changes dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -2599,54 +2635,54 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq -[23:17:28] This is snippy 4.6.0 -[23:17:28] Written by Torsten Seemann -[23:17:28] Obtained from https://github.com/tseemann/snippy -[23:17:28] Detected operating system: linux -[23:17:28] Enabling bundled linux tools. -[23:17:28] Found bwa - /usr/bin/bwa -[23:17:28] Found bcftools - /usr/bin/bcftools -[23:17:28] Found samtools - /usr/bin/samtools -[23:17:28] Found java - /usr/bin/java -[23:17:28] Found snpEff - /usr/bin/snpEff -[23:17:28] Found samclip - /usr/bin/samclip -[23:17:28] Found seqtk - /usr/bin/seqtk -[23:17:28] Found parallel - /usr/bin/parallel -[23:17:28] Found freebayes - /usr/bin/freebayes -[23:17:28] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:17:28] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:17:28] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:17:28] Found vcfuniq - /usr/bin/vcfuniq -[23:17:28] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:17:28] Found gzip - /usr/bin/gzip -[23:17:28] Found vt - /usr/bin/vt -[23:17:28] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:17:28] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:17:28] Checking version: samtools --version is >= 1.7 - ok, have 1.19 -[23:17:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[23:17:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[23:17:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:17:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 -[23:17:29] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:17:29] Treating reference as 'fasta' format. -[23:17:29] Will use 2 CPU cores. -[23:17:29] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq -[23:17:29] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[23:17:29] Used --force, will overwrite existing S1 -[23:17:29] Changing working directory: S1 -[23:17:29] Creating reference folder: reference -[23:17:29] Extracting FASTA and GFF from reference. -[23:17:29] Wrote 3 sequences to ref.fa -[23:17:29] Wrote 0 features to ref.gff -[23:17:29] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:17:29] Using BAM RG (Read Group) ID: S1 -[23:17:29] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:17:29] Running: bwa index reference/ref.fa 2>> snps.log -[23:17:30] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:17:30] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:17:30] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:17:30] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:17:30] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[07:46:40] This is snippy 4.6.0 +[07:46:40] Written by Torsten Seemann +[07:46:40] Obtained from https://github.com/tseemann/snippy +[07:46:40] Detected operating system: linux +[07:46:40] Enabling bundled linux tools. +[07:46:40] Found bwa - /usr/bin/bwa +[07:46:40] Found bcftools - /usr/bin/bcftools +[07:46:40] Found samtools - /usr/bin/samtools +[07:46:40] Found java - /usr/bin/java +[07:46:40] Found snpEff - /usr/bin/snpEff +[07:46:40] Found samclip - /usr/bin/samclip +[07:46:40] Found seqtk - /usr/bin/seqtk +[07:46:40] Found parallel - /usr/bin/parallel +[07:46:40] Found freebayes - /usr/bin/freebayes +[07:46:40] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[07:46:40] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[07:46:40] Found vcfstreamsort - /usr/bin/vcfstreamsort +[07:46:40] Found vcfuniq - /usr/bin/vcfuniq +[07:46:40] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[07:46:40] Found gzip - /usr/bin/gzip +[07:46:40] Found vt - /usr/bin/vt +[07:46:40] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[07:46:40] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[07:46:40] Checking version: samtools --version is >= 1.7 - ok, have 1.19 +[07:46:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[07:46:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[07:46:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[07:46:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 +[07:46:40] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[07:46:40] Treating reference as 'fasta' format. +[07:46:40] Will use 2 CPU cores. +[07:46:40] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq +[07:46:40] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[07:46:40] Used --force, will overwrite existing S1 +[07:46:40] Changing working directory: S1 +[07:46:40] Creating reference folder: reference +[07:46:40] Extracting FASTA and GFF from reference. +[07:46:40] Wrote 3 sequences to ref.fa +[07:46:40] Wrote 0 features to ref.gff +[07:46:40] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[07:46:40] Using BAM RG (Read Group) ID: S1 +[07:46:40] Running: samtools faidx reference/ref.fa 2>> snps.log +[07:46:40] Running: bwa index reference/ref.fa 2>> snps.log +[07:46:40] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[07:46:40] Running: ln -sf reference/ref.fa . 2>> snps.log +[07:46:40] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[07:46:40] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[07:46:40] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -2661,17 +2697,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 437) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 3.141 CPU sec, 3.405 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.462 CPU sec, 0.737 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[main] Real time: 4.330 sec; CPU: 3.256 sec +[main] Real time: 0.855 sec; CPU: 1.503 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 5 lines [samclip] Done. -[23:17:36] Running: samtools index snps.bam 2>> snps.log -[23:17:36] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:17:36] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[23:17:44] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[07:46:41] Running: samtools index snps.bam 2>> snps.log +[07:46:41] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[07:46:41] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[07:46:43] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2708,92 +2744,92 @@ Time elapsed: 0.01s -[23:17:44] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:17:44] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[23:17:45] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:17:45] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:17:45] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:17:45] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:17:45] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:17:45] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:17:45] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:17:45] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:17:45] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:17:47] Marked 749 heterozygous sites with 'n' -[23:17:47] Creating extra output files: BED GFF CSV TXT HTML -[23:17:47] Identified 261 variants. -[23:17:47] Result folder: S1 -[23:17:47] Result files: -[23:17:47] * S1/snps.aligned.fa -[23:17:47] * S1/snps.bam -[23:17:47] * S1/snps.bam.bai -[23:17:47] * S1/snps.bed -[23:17:47] * S1/snps.consensus.fa -[23:17:47] * S1/snps.consensus.subs.fa -[23:17:47] * S1/snps.csv -[23:17:47] * S1/snps.filt.vcf -[23:17:47] * S1/snps.gff -[23:17:47] * S1/snps.html -[23:17:47] * S1/snps.log -[23:17:47] * S1/snps.raw.vcf -[23:17:47] * S1/snps.subs.vcf -[23:17:47] * S1/snps.tab -[23:17:47] * S1/snps.txt -[23:17:47] * S1/snps.vcf -[23:17:47] * S1/snps.vcf.gz -[23:17:47] * S1/snps.vcf.gz.csi -[23:17:47] Walltime used: 19 seconds -[23:17:47] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md -[23:17:47] Done. +[07:46:43] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[07:46:43] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[07:46:43] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[07:46:43] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[07:46:43] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[07:46:43] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[07:46:43] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[07:46:43] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[07:46:43] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[07:46:43] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[07:46:43] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[07:46:43] Marked 749 heterozygous sites with 'n' +[07:46:43] Creating extra output files: BED GFF CSV TXT HTML +[07:46:43] Identified 261 variants. +[07:46:43] Result folder: S1 +[07:46:43] Result files: +[07:46:43] * S1/snps.aligned.fa +[07:46:43] * S1/snps.bam +[07:46:43] * S1/snps.bam.bai +[07:46:43] * S1/snps.bed +[07:46:43] * S1/snps.consensus.fa +[07:46:43] * S1/snps.consensus.subs.fa +[07:46:43] * S1/snps.csv +[07:46:43] * S1/snps.filt.vcf +[07:46:43] * S1/snps.gff +[07:46:43] * S1/snps.html +[07:46:43] * S1/snps.log +[07:46:43] * S1/snps.raw.vcf +[07:46:43] * S1/snps.subs.vcf +[07:46:43] * S1/snps.tab +[07:46:43] * S1/snps.txt +[07:46:43] * S1/snps.vcf +[07:46:43] * S1/snps.vcf.gz +[07:46:43] * S1/snps.vcf.gz.csi +[07:46:43] Walltime used: 3 seconds +[07:46:43] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues +[07:46:43] Done. ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq -[23:17:48] This is snippy 4.6.0 -[23:17:48] Written by Torsten Seemann -[23:17:48] Obtained from https://github.com/tseemann/snippy -[23:17:48] Detected operating system: linux -[23:17:48] Enabling bundled linux tools. -[23:17:48] Found bwa - /usr/bin/bwa -[23:17:48] Found bcftools - /usr/bin/bcftools -[23:17:48] Found samtools - /usr/bin/samtools -[23:17:48] Found java - /usr/bin/java -[23:17:48] Found snpEff - /usr/bin/snpEff -[23:17:48] Found samclip - /usr/bin/samclip -[23:17:48] Found seqtk - /usr/bin/seqtk -[23:17:48] Found parallel - /usr/bin/parallel -[23:17:48] Found freebayes - /usr/bin/freebayes -[23:17:48] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:17:48] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:17:48] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:17:48] Found vcfuniq - /usr/bin/vcfuniq -[23:17:48] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:17:48] Found gzip - /usr/bin/gzip -[23:17:48] Found vt - /usr/bin/vt -[23:17:48] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:17:48] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:17:48] Checking version: samtools --version is >= 1.7 - ok, have 1.19 -[23:17:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[23:17:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[23:17:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:17:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 -[23:17:49] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:17:49] Treating reference as 'fasta' format. -[23:17:49] Will use 2 CPU cores. -[23:17:49] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq -[23:17:49] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[23:17:49] Used --force, will overwrite existing S2 -[23:17:49] Changing working directory: S2 -[23:17:49] Creating reference folder: reference -[23:17:49] Extracting FASTA and GFF from reference. -[23:17:49] Wrote 3 sequences to ref.fa -[23:17:49] Wrote 0 features to ref.gff -[23:17:49] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:17:49] Using BAM RG (Read Group) ID: S2 -[23:17:49] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:17:49] Running: bwa index reference/ref.fa 2>> snps.log -[23:17:50] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:17:50] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:17:50] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:17:50] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:17:50] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[07:46:43] This is snippy 4.6.0 +[07:46:43] Written by Torsten Seemann +[07:46:43] Obtained from https://github.com/tseemann/snippy +[07:46:43] Detected operating system: linux +[07:46:43] Enabling bundled linux tools. +[07:46:43] Found bwa - /usr/bin/bwa +[07:46:43] Found bcftools - /usr/bin/bcftools +[07:46:43] Found samtools - /usr/bin/samtools +[07:46:43] Found java - /usr/bin/java +[07:46:43] Found snpEff - /usr/bin/snpEff +[07:46:43] Found samclip - /usr/bin/samclip +[07:46:43] Found seqtk - /usr/bin/seqtk +[07:46:43] Found parallel - /usr/bin/parallel +[07:46:43] Found freebayes - /usr/bin/freebayes +[07:46:43] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[07:46:43] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[07:46:43] Found vcfstreamsort - /usr/bin/vcfstreamsort +[07:46:43] Found vcfuniq - /usr/bin/vcfuniq +[07:46:43] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[07:46:43] Found gzip - /usr/bin/gzip +[07:46:43] Found vt - /usr/bin/vt +[07:46:43] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[07:46:43] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[07:46:43] Checking version: samtools --version is >= 1.7 - ok, have 1.19 +[07:46:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[07:46:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[07:46:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[07:46:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 +[07:46:43] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[07:46:43] Treating reference as 'fasta' format. +[07:46:43] Will use 2 CPU cores. +[07:46:43] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq +[07:46:43] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq +[07:46:43] Used --force, will overwrite existing S2 +[07:46:43] Changing working directory: S2 +[07:46:43] Creating reference folder: reference +[07:46:43] Extracting FASTA and GFF from reference. +[07:46:43] Wrote 3 sequences to ref.fa +[07:46:43] Wrote 0 features to ref.gff +[07:46:43] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[07:46:43] Using BAM RG (Read Group) ID: S2 +[07:46:43] Running: samtools faidx reference/ref.fa 2>> snps.log +[07:46:43] Running: bwa index reference/ref.fa 2>> snps.log +[07:46:44] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[07:46:44] Running: ln -sf reference/ref.fa . 2>> snps.log +[07:46:44] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[07:46:44] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[07:46:44] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -2808,17 +2844,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 3.142 CPU sec, 3.799 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.435 CPU sec, 0.724 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[main] Real time: 4.835 sec; CPU: 3.259 sec +[main] Real time: 0.840 sec; CPU: 1.470 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 5 lines [samclip] Done. -[23:17:57] Running: samtools index snps.bam 2>> snps.log -[23:17:57] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:17:57] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[23:18:01] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[07:46:45] Running: samtools index snps.bam 2>> snps.log +[07:46:45] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[07:46:45] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[07:46:46] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2853,99 +2889,99 @@ total no. variants observed : 246 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[23:18:01] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:18:01] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[23:18:02] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:18:02] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:18:02] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:18:02] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:18:02] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:18:02] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:18:02] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:18:02] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:18:02] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:18:03] Marked 841 heterozygous sites with 'n' -[23:18:03] Creating extra output files: BED GFF CSV TXT HTML -[23:18:03] Identified 246 variants. -[23:18:03] Result folder: S2 -[23:18:03] Result files: -[23:18:03] * S2/snps.aligned.fa -[23:18:03] * S2/snps.bam -[23:18:03] * S2/snps.bam.bai -[23:18:03] * S2/snps.bed -[23:18:03] * S2/snps.consensus.fa -[23:18:03] * S2/snps.consensus.subs.fa -[23:18:03] * S2/snps.csv -[23:18:03] * S2/snps.filt.vcf -[23:18:03] * S2/snps.gff -[23:18:03] * S2/snps.html -[23:18:03] * S2/snps.log -[23:18:03] * S2/snps.raw.vcf -[23:18:03] * S2/snps.subs.vcf -[23:18:03] * S2/snps.tab -[23:18:03] * S2/snps.txt -[23:18:03] * S2/snps.vcf -[23:18:03] * S2/snps.vcf.gz -[23:18:03] * S2/snps.vcf.gz.csi -[23:18:03] Walltime used: 15 seconds -[23:18:03] Questionable SNP? Try the --report option to see the alignments. -[23:18:03] Done. +[07:46:46] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[07:46:46] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[07:46:46] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[07:46:46] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[07:46:46] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[07:46:46] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[07:46:46] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[07:46:46] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[07:46:46] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[07:46:46] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[07:46:46] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[07:46:46] Marked 841 heterozygous sites with 'n' +[07:46:46] Creating extra output files: BED GFF CSV TXT HTML +[07:46:46] Identified 246 variants. +[07:46:46] Result folder: S2 +[07:46:46] Result files: +[07:46:46] * S2/snps.aligned.fa +[07:46:46] * S2/snps.bam +[07:46:46] * S2/snps.bam.bai +[07:46:46] * S2/snps.bed +[07:46:46] * S2/snps.consensus.fa +[07:46:46] * S2/snps.consensus.subs.fa +[07:46:46] * S2/snps.csv +[07:46:46] * S2/snps.filt.vcf +[07:46:46] * S2/snps.gff +[07:46:46] * S2/snps.html +[07:46:46] * S2/snps.log +[07:46:46] * S2/snps.raw.vcf +[07:46:46] * S2/snps.subs.vcf +[07:46:46] * S2/snps.tab +[07:46:46] * S2/snps.txt +[07:46:46] * S2/snps.vcf +[07:46:46] * S2/snps.vcf.gz +[07:46:46] * S2/snps.vcf.gz.csi +[07:46:46] Walltime used: 3 seconds +[07:46:46] Did you know? Snippy is a combination of SNP, Skippy, and snappy. +[07:46:46] Done. ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq -[23:18:03] This is snippy 4.6.0 -[23:18:03] Written by Torsten Seemann -[23:18:03] Obtained from https://github.com/tseemann/snippy -[23:18:03] Detected operating system: linux -[23:18:03] Enabling bundled linux tools. -[23:18:03] Found bwa - /usr/bin/bwa -[23:18:03] Found bcftools - /usr/bin/bcftools -[23:18:03] Found samtools - /usr/bin/samtools -[23:18:03] Found java - /usr/bin/java -[23:18:03] Found snpEff - /usr/bin/snpEff -[23:18:03] Found samclip - /usr/bin/samclip -[23:18:03] Found seqtk - /usr/bin/seqtk -[23:18:03] Found parallel - /usr/bin/parallel -[23:18:03] Found freebayes - /usr/bin/freebayes -[23:18:03] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:18:03] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:18:03] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:18:03] Found vcfuniq - /usr/bin/vcfuniq -[23:18:03] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:18:03] Found gzip - /usr/bin/gzip -[23:18:03] Found vt - /usr/bin/vt -[23:18:03] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:18:03] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:18:03] Checking version: samtools --version is >= 1.7 - ok, have 1.19 -[23:18:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[23:18:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[23:18:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:18:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 -[23:18:03] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:18:03] Treating reference as 'fasta' format. -[23:18:03] Will use 2 CPU cores. -[23:18:03] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq -[23:18:03] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[23:18:03] Used --force, will overwrite existing S3 -[23:18:03] Changing working directory: S3 -[23:18:03] Creating reference folder: reference -[23:18:03] Extracting FASTA and GFF from reference. -[23:18:03] Wrote 3 sequences to ref.fa -[23:18:03] Wrote 0 features to ref.gff -[23:18:03] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:18:03] Using BAM RG (Read Group) ID: S3 -[23:18:03] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:18:03] Running: bwa index reference/ref.fa 2>> snps.log -[23:18:04] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:18:04] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:18:04] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:18:04] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:18:04] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[07:46:47] This is snippy 4.6.0 +[07:46:47] Written by Torsten Seemann +[07:46:47] Obtained from https://github.com/tseemann/snippy +[07:46:47] Detected operating system: linux +[07:46:47] Enabling bundled linux tools. +[07:46:47] Found bwa - /usr/bin/bwa +[07:46:47] Found bcftools - /usr/bin/bcftools +[07:46:47] Found samtools - /usr/bin/samtools +[07:46:47] Found java - /usr/bin/java +[07:46:47] Found snpEff - /usr/bin/snpEff +[07:46:47] Found samclip - /usr/bin/samclip +[07:46:47] Found seqtk - /usr/bin/seqtk +[07:46:47] Found parallel - /usr/bin/parallel +[07:46:47] Found freebayes - /usr/bin/freebayes +[07:46:47] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[07:46:47] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[07:46:47] Found vcfstreamsort - /usr/bin/vcfstreamsort +[07:46:47] Found vcfuniq - /usr/bin/vcfuniq +[07:46:47] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[07:46:47] Found gzip - /usr/bin/gzip +[07:46:47] Found vt - /usr/bin/vt +[07:46:47] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[07:46:47] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[07:46:47] Checking version: samtools --version is >= 1.7 - ok, have 1.19 +[07:46:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[07:46:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[07:46:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[07:46:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 +[07:46:47] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[07:46:47] Treating reference as 'fasta' format. +[07:46:47] Will use 2 CPU cores. +[07:46:47] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq +[07:46:47] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[07:46:47] Used --force, will overwrite existing S3 +[07:46:47] Changing working directory: S3 +[07:46:47] Creating reference folder: reference +[07:46:47] Extracting FASTA and GFF from reference. +[07:46:47] Wrote 3 sequences to ref.fa +[07:46:47] Wrote 0 features to ref.gff +[07:46:47] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[07:46:47] Using BAM RG (Read Group) ID: S3 +[07:46:47] Running: samtools faidx reference/ref.fa 2>> snps.log +[07:46:47] Running: bwa index reference/ref.fa 2>> snps.log +[07:46:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[07:46:47] Running: ln -sf reference/ref.fa . 2>> snps.log +[07:46:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[07:46:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[07:46:47] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs +[M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai -[M::process] read 24000 sequences (2400000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... @@ -2955,17 +2991,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 2.889 CPU sec, 1.646 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.449 CPU sec, 0.727 real sec [main] Version: 0.7.17-r1188 -[main] CMD:[samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 +[main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[main] Real time: 0.842 sec; CPU: 1.489 sec +[samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 5 lines [samclip] Done. - bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[main] Real time: 2.001 sec; CPU: 2.991 sec -[23:18:07] Running: samtools index snps.bam 2>> snps.log -[23:18:07] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:18:07] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[23:18:11] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[07:46:48] Running: samtools index snps.bam 2>> snps.log +[07:46:48] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[07:46:48] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[07:46:49] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -3002,92 +3038,92 @@ Time elapsed: 0.01s -[23:18:11] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:18:11] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[23:18:12] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:18:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:18:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:18:12] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:18:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:18:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:18:12] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:18:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:18:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:18:13] Marked 846 heterozygous sites with 'n' -[23:18:13] Creating extra output files: BED GFF CSV TXT HTML -[23:18:13] Identified 254 variants. -[23:18:13] Result folder: S3 -[23:18:13] Result files: -[23:18:13] * S3/snps.aligned.fa -[23:18:13] * S3/snps.bam -[23:18:13] * S3/snps.bam.bai -[23:18:13] * S3/snps.bed -[23:18:13] * S3/snps.consensus.fa -[23:18:13] * S3/snps.consensus.subs.fa -[23:18:13] * S3/snps.csv -[23:18:13] * S3/snps.filt.vcf -[23:18:13] * S3/snps.gff -[23:18:13] * S3/snps.html -[23:18:13] * S3/snps.log -[23:18:13] * S3/snps.raw.vcf -[23:18:13] * S3/snps.subs.vcf -[23:18:13] * S3/snps.tab -[23:18:13] * S3/snps.txt -[23:18:13] * S3/snps.vcf -[23:18:13] * S3/snps.vcf.gz -[23:18:13] * S3/snps.vcf.gz.csi -[23:18:13] Walltime used: 10 seconds -[23:18:13] Found a bug? Post it at https://github.com/tseemann/snippy/issues -[23:18:13] Done. +[07:46:49] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[07:46:49] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[07:46:49] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[07:46:49] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[07:46:49] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[07:46:49] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[07:46:49] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[07:46:49] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[07:46:49] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[07:46:49] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[07:46:49] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[07:46:50] Marked 846 heterozygous sites with 'n' +[07:46:50] Creating extra output files: BED GFF CSV TXT HTML +[07:46:50] Identified 254 variants. +[07:46:50] Result folder: S3 +[07:46:50] Result files: +[07:46:50] * S3/snps.aligned.fa +[07:46:50] * S3/snps.bam +[07:46:50] * S3/snps.bam.bai +[07:46:50] * S3/snps.bed +[07:46:50] * S3/snps.consensus.fa +[07:46:50] * S3/snps.consensus.subs.fa +[07:46:50] * S3/snps.csv +[07:46:50] * S3/snps.filt.vcf +[07:46:50] * S3/snps.gff +[07:46:50] * S3/snps.html +[07:46:50] * S3/snps.log +[07:46:50] * S3/snps.raw.vcf +[07:46:50] * S3/snps.subs.vcf +[07:46:50] * S3/snps.tab +[07:46:50] * S3/snps.txt +[07:46:50] * S3/snps.vcf +[07:46:50] * S3/snps.vcf.gz +[07:46:50] * S3/snps.vcf.gz.csi +[07:46:50] Walltime used: 3 seconds +[07:46:50] May the SNPs be with you. +[07:46:50] Done. ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq -[23:18:13] This is snippy 4.6.0 -[23:18:13] Written by Torsten Seemann -[23:18:13] Obtained from https://github.com/tseemann/snippy -[23:18:13] Detected operating system: linux -[23:18:13] Enabling bundled linux tools. -[23:18:13] Found bwa - /usr/bin/bwa -[23:18:13] Found bcftools - /usr/bin/bcftools -[23:18:13] Found samtools - /usr/bin/samtools -[23:18:13] Found java - /usr/bin/java -[23:18:13] Found snpEff - /usr/bin/snpEff -[23:18:13] Found samclip - /usr/bin/samclip -[23:18:13] Found seqtk - /usr/bin/seqtk -[23:18:13] Found parallel - /usr/bin/parallel -[23:18:13] Found freebayes - /usr/bin/freebayes -[23:18:13] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:18:13] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:18:13] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:18:13] Found vcfuniq - /usr/bin/vcfuniq -[23:18:13] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:18:13] Found gzip - /usr/bin/gzip -[23:18:13] Found vt - /usr/bin/vt -[23:18:13] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:18:13] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:18:13] Checking version: samtools --version is >= 1.7 - ok, have 1.19 -[23:18:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[23:18:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[23:18:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:18:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 -[23:18:14] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:18:14] Treating reference as 'fasta' format. -[23:18:14] Will use 2 CPU cores. -[23:18:14] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq -[23:18:14] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[23:18:14] Used --force, will overwrite existing S4 -[23:18:14] Changing working directory: S4 -[23:18:14] Creating reference folder: reference -[23:18:14] Extracting FASTA and GFF from reference. -[23:18:14] Wrote 3 sequences to ref.fa -[23:18:14] Wrote 0 features to ref.gff -[23:18:14] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:18:14] Using BAM RG (Read Group) ID: S4 -[23:18:14] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:18:14] Running: bwa index reference/ref.fa 2>> snps.log -[23:18:14] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:18:14] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:18:14] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:18:14] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:18:14] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[07:46:50] This is snippy 4.6.0 +[07:46:50] Written by Torsten Seemann +[07:46:50] Obtained from https://github.com/tseemann/snippy +[07:46:50] Detected operating system: linux +[07:46:50] Enabling bundled linux tools. +[07:46:50] Found bwa - /usr/bin/bwa +[07:46:50] Found bcftools - /usr/bin/bcftools +[07:46:50] Found samtools - /usr/bin/samtools +[07:46:50] Found java - /usr/bin/java +[07:46:50] Found snpEff - /usr/bin/snpEff +[07:46:50] Found samclip - /usr/bin/samclip +[07:46:50] Found seqtk - /usr/bin/seqtk +[07:46:50] Found parallel - /usr/bin/parallel +[07:46:50] Found freebayes - /usr/bin/freebayes +[07:46:50] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[07:46:50] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[07:46:50] Found vcfstreamsort - /usr/bin/vcfstreamsort +[07:46:50] Found vcfuniq - /usr/bin/vcfuniq +[07:46:50] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[07:46:50] Found gzip - /usr/bin/gzip +[07:46:50] Found vt - /usr/bin/vt +[07:46:50] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[07:46:50] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[07:46:50] Checking version: samtools --version is >= 1.7 - ok, have 1.19 +[07:46:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[07:46:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[07:46:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[07:46:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 +[07:46:50] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[07:46:50] Treating reference as 'fasta' format. +[07:46:50] Will use 2 CPU cores. +[07:46:50] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq +[07:46:50] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[07:46:50] Used --force, will overwrite existing S4 +[07:46:50] Changing working directory: S4 +[07:46:50] Creating reference folder: reference +[07:46:50] Extracting FASTA and GFF from reference. +[07:46:50] Wrote 3 sequences to ref.fa +[07:46:50] Wrote 0 features to ref.gff +[07:46:50] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[07:46:50] Using BAM RG (Read Group) ID: S4 +[07:46:50] Running: samtools faidx reference/ref.fa 2>> snps.log +[07:46:50] Running: bwa index reference/ref.fa 2>> snps.log +[07:46:50] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[07:46:50] Running: ln -sf reference/ref.fa . 2>> snps.log +[07:46:50] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[07:46:50] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[07:46:50] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -3102,17 +3138,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 2.953 CPU sec, 1.508 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.433 CPU sec, 0.721 real sec [main] Version: 0.7.17-r1188 -[main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[main] Real time: 1.772 sec; CPU: 3.058 sec -[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 +[main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 5 lines [samclip] Done. -[23:18:17] Running: samtools index snps.bam 2>> snps.log -[23:18:17] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:18:17] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[23:18:20] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log + +[main] Real time: 0.839 sec; CPU: 1.472 sec +[07:46:51] Running: samtools index snps.bam 2>> snps.log +[07:46:51] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[07:46:51] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[07:46:52] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -3147,45 +3183,45 @@ total no. variants observed : 257 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[23:18:21] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:18:21] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[23:18:21] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:18:21] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:18:21] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:18:22] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:18:22] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:18:22] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:18:22] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:18:22] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:18:22] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:18:23] Marked 799 heterozygous sites with 'n' -[23:18:23] Creating extra output files: BED GFF CSV TXT HTML -[23:18:23] Identified 257 variants. -[23:18:23] Result folder: S4 -[23:18:23] Result files: -[23:18:23] * S4/snps.aligned.fa -[23:18:23] * S4/snps.bam -[23:18:23] * S4/snps.bam.bai -[23:18:23] * S4/snps.bed -[23:18:23] * S4/snps.consensus.fa -[23:18:23] * S4/snps.consensus.subs.fa -[23:18:23] * S4/snps.csv -[23:18:23] * S4/snps.filt.vcf -[23:18:23] * S4/snps.gff -[23:18:23] * S4/snps.html -[23:18:23] * S4/snps.log -[23:18:23] * S4/snps.raw.vcf -[23:18:23] * S4/snps.subs.vcf -[23:18:23] * S4/snps.tab -[23:18:23] * S4/snps.txt -[23:18:23] * S4/snps.vcf -[23:18:23] * S4/snps.vcf.gz -[23:18:23] * S4/snps.vcf.gz.csi -[23:18:23] Walltime used: 10 seconds -[23:18:23] Found a bug? Post it at https://github.com/tseemann/snippy/issues -[23:18:23] Done. +[07:46:52] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[07:46:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[07:46:53] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[07:46:53] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[07:46:53] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[07:46:53] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[07:46:53] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[07:46:53] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[07:46:53] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[07:46:53] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[07:46:53] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[07:46:53] Marked 799 heterozygous sites with 'n' +[07:46:53] Creating extra output files: BED GFF CSV TXT HTML +[07:46:53] Identified 257 variants. +[07:46:53] Result folder: S4 +[07:46:53] Result files: +[07:46:53] * S4/snps.aligned.fa +[07:46:53] * S4/snps.bam +[07:46:53] * S4/snps.bam.bai +[07:46:53] * S4/snps.bed +[07:46:53] * S4/snps.consensus.fa +[07:46:53] * S4/snps.consensus.subs.fa +[07:46:53] * S4/snps.csv +[07:46:53] * S4/snps.filt.vcf +[07:46:53] * S4/snps.gff +[07:46:53] * S4/snps.html +[07:46:53] * S4/snps.log +[07:46:53] * S4/snps.raw.vcf +[07:46:53] * S4/snps.subs.vcf +[07:46:53] * S4/snps.tab +[07:46:53] * S4/snps.txt +[07:46:53] * S4/snps.vcf +[07:46:53] * S4/snps.vcf.gz +[07:46:53] * S4/snps.vcf.gz.csi +[07:46:53] Walltime used: 3 seconds +[07:46:53] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md +[07:46:53] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 @@ -3218,7 +3254,7 @@ Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln -You can mask columns using '--mask BEDFILE --mask-char X' +This analysis is totally hard-core! Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy @@ -3252,7 +3288,7 @@ Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln -The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md +Run 'snp-sites -b -c -o phylo.aln core.full.aln' for IQTree, BEAST, RaxML Done. wc -l S?/snps.tab 262 S1/snps.tab @@ -3290,12 +3326,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3099667/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1133945 and its subdirectories -I: Current time: Tue May 28 23:18:38 -12 2024 -I: pbuilder-time-stamp: 1716981518 +I: removing directory /srv/workspace/pbuilder/3099667 and its subdirectories +I: Current time: Wed Jul 2 07:46:58 +14 2025 +I: pbuilder-time-stamp: 1751392018