Diff of the two buildlogs: -- --- b1/build.log 2025-09-11 11:20:36.508357074 +0000 +++ b2/build.log 2025-09-11 11:26:07.660773946 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 14 05:31:38 -12 2026 -I: pbuilder-time-stamp: 1791999098 +I: Current time: Fri Sep 12 01:20:37 +14 2025 +I: pbuilder-time-stamp: 1757589637 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying make-4.4.1.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3313594/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1551041/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Sep 11 11:20 /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/1551041/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1551041/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=42 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='5994fe667db24b24997e71bc642630b7' - 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='3313594' - PS1='# ' - PS2='> ' + INVOCATION_ID=97840733cf624bb8afc1e0641b569e80 + 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=1551041 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.QY1zjnqs/pbuilderrc_zKFE --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QY1zjnqs/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.QY1zjnqs/pbuilderrc_4xn9 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QY1zjnqs/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3313594/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1551041/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -554,7 +586,7 @@ Get: 413 http://deb.debian.org/debian forky/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB] Get: 414 http://deb.debian.org/debian forky/main amd64 snpeff all 5.2.f+dfsg-1 [7244 B] Get: 415 http://deb.debian.org/debian forky/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] -Fetched 329 MB in 31s (10.5 MB/s) +Fetched 329 MB in 3s (94.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared: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 ... 21054 files and directories currently installed.) @@ -1919,8 +1951,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Oct 14 17:39:56 UTC 2026. -Universal Time is now: Wed Oct 14 17:39:56 UTC 2026. +Local time is now: Thu Sep 11 11:25:05 UTC 2025. +Universal Time is now: Thu Sep 11 11:25:05 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2444,7 +2476,11 @@ 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-5_source.changes +I: user script /srv/workspace/pbuilder/1551041/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1551041/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-5_source.changes dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -2470,54 +2506,54 @@ [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 -[05:42:06] This is snippy 4.6.0 -[05:42:06] Written by Torsten Seemann -[05:42:06] Obtained from https://github.com/tseemann/snippy -[05:42:06] Detected operating system: linux -[05:42:06] Enabling bundled linux tools. -[05:42:06] Found bwa - /usr/bin/bwa -[05:42:06] Found bcftools - /usr/bin/bcftools -[05:42:06] Found samtools - /usr/bin/samtools -[05:42:06] Found java - /usr/bin/java -[05:42:06] Found snpEff - /usr/bin/snpEff -[05:42:06] Found samclip - /usr/bin/samclip -[05:42:06] Found seqtk - /usr/bin/seqtk -[05:42:06] Found parallel - /usr/bin/parallel -[05:42:06] Found freebayes - /usr/bin/freebayes -[05:42:06] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[05:42:06] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[05:42:06] Found vcfstreamsort - /usr/bin/vcfstreamsort -[05:42:06] Found vcfuniq - /usr/bin/vcfuniq -[05:42:06] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[05:42:06] Found gzip - /usr/bin/gzip -[05:42:06] Found vt - /usr/bin/vt -[05:42:06] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[05:42:06] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[05:42:06] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[05:42:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[05:42:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[05:42:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[05:42:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[05:42:07] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[05:42:07] Treating reference as 'fasta' format. -[05:42:07] Will use 2 CPU cores. -[05:42:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq -[05:42:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[05:42:07] Used --force, will overwrite existing S1 -[05:42:07] Changing working directory: S1 -[05:42:07] Creating reference folder: reference -[05:42:07] Extracting FASTA and GFF from reference. -[05:42:07] Wrote 3 sequences to ref.fa -[05:42:07] Wrote 0 features to ref.gff -[05:42:07] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[05:42:07] Using BAM RG (Read Group) ID: S1 -[05:42:07] Running: samtools faidx reference/ref.fa 2>> snps.log -[05:42:07] Running: bwa index reference/ref.fa 2>> snps.log -[05:42:08] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[05:42:08] Running: ln -sf reference/ref.fa . 2>> snps.log -[05:42:08] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[05:42:08] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[05:42:08] 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 +[01:25:44] This is snippy 4.6.0 +[01:25:44] Written by Torsten Seemann +[01:25:44] Obtained from https://github.com/tseemann/snippy +[01:25:44] Detected operating system: linux +[01:25:44] Enabling bundled linux tools. +[01:25:44] Found bwa - /usr/bin/bwa +[01:25:44] Found bcftools - /usr/bin/bcftools +[01:25:44] Found samtools - /usr/bin/samtools +[01:25:44] Found java - /usr/bin/java +[01:25:44] Found snpEff - /usr/bin/snpEff +[01:25:44] Found samclip - /usr/bin/samclip +[01:25:44] Found seqtk - /usr/bin/seqtk +[01:25:44] Found parallel - /usr/bin/parallel +[01:25:44] Found freebayes - /usr/bin/freebayes +[01:25:44] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[01:25:44] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[01:25:44] Found vcfstreamsort - /usr/bin/vcfstreamsort +[01:25:44] Found vcfuniq - /usr/bin/vcfuniq +[01:25:44] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[01:25:44] Found gzip - /usr/bin/gzip +[01:25:44] Found vt - /usr/bin/vt +[01:25:44] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[01:25:44] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[01:25:44] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[01:25:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[01:25:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[01:25:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[01:25:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[01:25:44] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[01:25:44] Treating reference as 'fasta' format. +[01:25:44] Will use 2 CPU cores. +[01:25:44] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq +[01:25:44] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[01:25:44] Used --force, will overwrite existing S1 +[01:25:44] Changing working directory: S1 +[01:25:44] Creating reference folder: reference +[01:25:44] Extracting FASTA and GFF from reference. +[01:25:44] Wrote 3 sequences to ref.fa +[01:25:44] Wrote 0 features to ref.gff +[01:25:44] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[01:25:44] Using BAM RG (Read Group) ID: S1 +[01:25:44] Running: samtools faidx reference/ref.fa 2>> snps.log +[01:25:44] Running: bwa index reference/ref.fa 2>> snps.log +[01:25:45] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[01:25:45] Running: ln -sf reference/ref.fa . 2>> snps.log +[01:25:45] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[01:25:45] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[01:25:45] 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) @@ -2532,17 +2568,17 @@ [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 2.364 CPU sec, 2.217 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.344 CPU sec, 0.673 real sec [main] Version: 0.7.19-r1273 -[main] CMD:[samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 +[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: 0.805 sec; CPU: 1.390 sec +[samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. - 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: 2.584 sec; CPU: 2.430 sec -[05:42:12] Running: samtools index snps.bam 2>> snps.log -[05:42:13] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[05:42:15] 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 -[05:42:19] 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 +[01:25:46] Running: samtools index snps.bam 2>> snps.log +[01:25:46] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[01:25:46] 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 +[01:25:47] 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 - @@ -2577,45 +2613,45 @@ total no. variants observed : 261 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[05:42:19] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[05:42:19] 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 -[05:42:19] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[05:42:19] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[05:42:20] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[05:42:20] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[05:42:20] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[05:42:20] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[05:42:20] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[05:42:20] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[05:42:20] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[05:42:20] Marked 749 heterozygous sites with 'n' -[05:42:20] Creating extra output files: BED GFF CSV TXT HTML -[05:42:20] Identified 261 variants. -[05:42:20] Result folder: S1 -[05:42:20] Result files: -[05:42:20] * S1/snps.aligned.fa -[05:42:20] * S1/snps.bam -[05:42:20] * S1/snps.bam.bai -[05:42:20] * S1/snps.bed -[05:42:20] * S1/snps.consensus.fa -[05:42:20] * S1/snps.consensus.subs.fa -[05:42:20] * S1/snps.csv -[05:42:20] * S1/snps.filt.vcf -[05:42:20] * S1/snps.gff -[05:42:20] * S1/snps.html -[05:42:20] * S1/snps.log -[05:42:20] * S1/snps.raw.vcf -[05:42:20] * S1/snps.subs.vcf -[05:42:20] * S1/snps.tab -[05:42:20] * S1/snps.txt -[05:42:20] * S1/snps.vcf -[05:42:20] * S1/snps.vcf.gz -[05:42:20] * S1/snps.vcf.gz.csi -[05:42:20] Walltime used: 14 seconds -[05:42:20] Wishing you a life free of homopolymer errors. -[05:42:20] Done. +[01:25:47] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[01:25:47] 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 +[01:25:47] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[01:25:47] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[01:25:47] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[01:25:47] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[01:25:47] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[01:25:47] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[01:25:47] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[01:25:47] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[01:25:47] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[01:25:47] Marked 749 heterozygous sites with 'n' +[01:25:47] Creating extra output files: BED GFF CSV TXT HTML +[01:25:47] Identified 261 variants. +[01:25:47] Result folder: S1 +[01:25:47] Result files: +[01:25:47] * S1/snps.aligned.fa +[01:25:47] * S1/snps.bam +[01:25:47] * S1/snps.bam.bai +[01:25:47] * S1/snps.bed +[01:25:47] * S1/snps.consensus.fa +[01:25:47] * S1/snps.consensus.subs.fa +[01:25:47] * S1/snps.csv +[01:25:47] * S1/snps.filt.vcf +[01:25:47] * S1/snps.gff +[01:25:47] * S1/snps.html +[01:25:47] * S1/snps.log +[01:25:47] * S1/snps.raw.vcf +[01:25:47] * S1/snps.subs.vcf +[01:25:47] * S1/snps.tab +[01:25:47] * S1/snps.txt +[01:25:47] * S1/snps.vcf +[01:25:47] * S1/snps.vcf.gz +[01:25:47] * S1/snps.vcf.gz.csi +[01:25:47] Walltime used: 3 seconds +[01:25:47] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md +[01:25:47] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2624,54 +2660,54 @@ [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 S2 --R1 S2/R1.fq --R2 S2/R2.fq -[05:42:24] This is snippy 4.6.0 -[05:42:24] Written by Torsten Seemann -[05:42:24] Obtained from https://github.com/tseemann/snippy -[05:42:24] Detected operating system: linux -[05:42:24] Enabling bundled linux tools. -[05:42:24] Found bwa - /usr/bin/bwa -[05:42:24] Found bcftools - /usr/bin/bcftools -[05:42:24] Found samtools - /usr/bin/samtools -[05:42:24] Found java - /usr/bin/java -[05:42:24] Found snpEff - /usr/bin/snpEff -[05:42:24] Found samclip - /usr/bin/samclip -[05:42:24] Found seqtk - /usr/bin/seqtk -[05:42:24] Found parallel - /usr/bin/parallel -[05:42:24] Found freebayes - /usr/bin/freebayes -[05:42:24] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[05:42:24] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[05:42:24] Found vcfstreamsort - /usr/bin/vcfstreamsort -[05:42:24] Found vcfuniq - /usr/bin/vcfuniq -[05:42:24] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[05:42:24] Found gzip - /usr/bin/gzip -[05:42:24] Found vt - /usr/bin/vt -[05:42:24] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[05:42:24] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[05:42:24] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[05:42:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[05:42:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[05:42:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[05:42:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[05:42:25] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[05:42:25] Treating reference as 'fasta' format. -[05:42:25] Will use 2 CPU cores. -[05:42:25] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq -[05:42:25] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[05:42:25] Used --force, will overwrite existing S2 -[05:42:25] Changing working directory: S2 -[05:42:25] Creating reference folder: reference -[05:42:25] Extracting FASTA and GFF from reference. -[05:42:25] Wrote 3 sequences to ref.fa -[05:42:25] Wrote 0 features to ref.gff -[05:42:25] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[05:42:25] Using BAM RG (Read Group) ID: S2 -[05:42:25] Running: samtools faidx reference/ref.fa 2>> snps.log -[05:42:25] Running: bwa index reference/ref.fa 2>> snps.log -[05:42:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[05:42:26] Running: ln -sf reference/ref.fa . 2>> snps.log -[05:42:26] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[05:42:26] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[05:42:26] 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 +[01:25:48] This is snippy 4.6.0 +[01:25:48] Written by Torsten Seemann +[01:25:48] Obtained from https://github.com/tseemann/snippy +[01:25:48] Detected operating system: linux +[01:25:48] Enabling bundled linux tools. +[01:25:48] Found bwa - /usr/bin/bwa +[01:25:48] Found bcftools - /usr/bin/bcftools +[01:25:48] Found samtools - /usr/bin/samtools +[01:25:48] Found java - /usr/bin/java +[01:25:48] Found snpEff - /usr/bin/snpEff +[01:25:48] Found samclip - /usr/bin/samclip +[01:25:48] Found seqtk - /usr/bin/seqtk +[01:25:48] Found parallel - /usr/bin/parallel +[01:25:48] Found freebayes - /usr/bin/freebayes +[01:25:48] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[01:25:48] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[01:25:48] Found vcfstreamsort - /usr/bin/vcfstreamsort +[01:25:48] Found vcfuniq - /usr/bin/vcfuniq +[01:25:48] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[01:25:48] Found gzip - /usr/bin/gzip +[01:25:48] Found vt - /usr/bin/vt +[01:25:48] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[01:25:48] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[01:25:48] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[01:25:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[01:25:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[01:25:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[01:25:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[01:25:48] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[01:25:48] Treating reference as 'fasta' format. +[01:25:48] Will use 2 CPU cores. +[01:25:48] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq +[01:25:48] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq +[01:25:48] Used --force, will overwrite existing S2 +[01:25:48] Changing working directory: S2 +[01:25:48] Creating reference folder: reference +[01:25:48] Extracting FASTA and GFF from reference. +[01:25:48] Wrote 3 sequences to ref.fa +[01:25:48] Wrote 0 features to ref.gff +[01:25:48] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[01:25:48] Using BAM RG (Read Group) ID: S2 +[01:25:48] Running: samtools faidx reference/ref.fa 2>> snps.log +[01:25:48] Running: bwa index reference/ref.fa 2>> snps.log +[01:25:48] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[01:25:48] Running: ln -sf reference/ref.fa . 2>> snps.log +[01:25:48] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[01:25:48] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[01:25:48] 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) @@ -2686,17 +2722,17 @@ [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 2.227 CPU sec, 1.404 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.352 CPU sec, 0.677 real sec [main] Version: 0.7.19-r1273 -[main] CMD: bwa mem[samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 - -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: 1.723 sec; CPU: 2.297 sec +[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: 0.788 sec; CPU: 1.394 sec +[samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. -[05:42:29] Running: samtools index snps.bam 2>> snps.log -[05:42:29] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[05:42:29] 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 -[05:42:35] 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 +[01:25:49] Running: samtools index snps.bam 2>> snps.log +[01:25:49] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[01:25:49] 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 +[01:25:50] 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 - @@ -2731,45 +2767,45 @@ total no. variants observed : 246 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[05:42:35] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[05:42:35] 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 -[05:42:35] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[05:42:35] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[05:42:35] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[05:42:35] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[05:42:35] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[05:42:35] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[05:42:35] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[05:42:35] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[05:42:35] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[05:42:37] Marked 841 heterozygous sites with 'n' -[05:42:37] Creating extra output files: BED GFF CSV TXT HTML -[05:42:37] Identified 246 variants. -[05:42:37] Result folder: S2 -[05:42:37] Result files: -[05:42:37] * S2/snps.aligned.fa -[05:42:37] * S2/snps.bam -[05:42:37] * S2/snps.bam.bai -[05:42:37] * S2/snps.bed -[05:42:37] * S2/snps.consensus.fa -[05:42:37] * S2/snps.consensus.subs.fa -[05:42:37] * S2/snps.csv -[05:42:37] * S2/snps.filt.vcf -[05:42:37] * S2/snps.gff -[05:42:37] * S2/snps.html -[05:42:37] * S2/snps.log -[05:42:37] * S2/snps.raw.vcf -[05:42:37] * S2/snps.subs.vcf -[05:42:37] * S2/snps.tab -[05:42:37] * S2/snps.txt -[05:42:37] * S2/snps.vcf -[05:42:37] * S2/snps.vcf.gz -[05:42:37] * S2/snps.vcf.gz.csi -[05:42:37] Walltime used: 13 seconds -[05:42:37] Found a bug? Post it at https://github.com/tseemann/snippy/issues -[05:42:37] Done. +[01:25:51] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[01:25:51] 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 +[01:25:51] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[01:25:51] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[01:25:51] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[01:25:51] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[01:25:51] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[01:25:51] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[01:25:51] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[01:25:51] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[01:25:51] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[01:25:51] Marked 841 heterozygous sites with 'n' +[01:25:51] Creating extra output files: BED GFF CSV TXT HTML +[01:25:51] Identified 246 variants. +[01:25:51] Result folder: S2 +[01:25:51] Result files: +[01:25:51] * S2/snps.aligned.fa +[01:25:51] * S2/snps.bam +[01:25:51] * S2/snps.bam.bai +[01:25:51] * S2/snps.bed +[01:25:51] * S2/snps.consensus.fa +[01:25:51] * S2/snps.consensus.subs.fa +[01:25:51] * S2/snps.csv +[01:25:51] * S2/snps.filt.vcf +[01:25:51] * S2/snps.gff +[01:25:51] * S2/snps.html +[01:25:51] * S2/snps.log +[01:25:51] * S2/snps.raw.vcf +[01:25:51] * S2/snps.subs.vcf +[01:25:51] * S2/snps.tab +[01:25:51] * S2/snps.txt +[01:25:51] * S2/snps.vcf +[01:25:51] * S2/snps.vcf.gz +[01:25:51] * S2/snps.vcf.gz.csi +[01:25:51] Walltime used: 3 seconds +[01:25:51] Questionable SNP? Try the --report option to see the alignments. +[01:25:51] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2778,54 +2814,54 @@ [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 S3 --R1 S3/R1.fq --R2 S3/R2.fq -[05:42:37] This is snippy 4.6.0 -[05:42:37] Written by Torsten Seemann -[05:42:37] Obtained from https://github.com/tseemann/snippy -[05:42:37] Detected operating system: linux -[05:42:37] Enabling bundled linux tools. -[05:42:37] Found bwa - /usr/bin/bwa -[05:42:37] Found bcftools - /usr/bin/bcftools -[05:42:37] Found samtools - /usr/bin/samtools -[05:42:37] Found java - /usr/bin/java -[05:42:37] Found snpEff - /usr/bin/snpEff -[05:42:37] Found samclip - /usr/bin/samclip -[05:42:37] Found seqtk - /usr/bin/seqtk -[05:42:37] Found parallel - /usr/bin/parallel -[05:42:37] Found freebayes - /usr/bin/freebayes -[05:42:37] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[05:42:37] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[05:42:37] Found vcfstreamsort - /usr/bin/vcfstreamsort -[05:42:37] Found vcfuniq - /usr/bin/vcfuniq -[05:42:37] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[05:42:37] Found gzip - /usr/bin/gzip -[05:42:37] Found vt - /usr/bin/vt -[05:42:37] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[05:42:37] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[05:42:37] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[05:42:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[05:42:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[05:42:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[05:42:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[05:42:38] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[05:42:38] Treating reference as 'fasta' format. -[05:42:38] Will use 2 CPU cores. -[05:42:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq -[05:42:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[05:42:38] Used --force, will overwrite existing S3 -[05:42:38] Changing working directory: S3 -[05:42:38] Creating reference folder: reference -[05:42:38] Extracting FASTA and GFF from reference. -[05:42:38] Wrote 3 sequences to ref.fa -[05:42:38] Wrote 0 features to ref.gff -[05:42:38] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[05:42:38] Using BAM RG (Read Group) ID: S3 -[05:42:38] Running: samtools faidx reference/ref.fa 2>> snps.log -[05:42:39] Running: bwa index reference/ref.fa 2>> snps.log -[05:42:41] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[05:42:41] Running: ln -sf reference/ref.fa . 2>> snps.log -[05:42:41] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[05:42:41] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[05:42:41] 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 +[01:25:51] This is snippy 4.6.0 +[01:25:51] Written by Torsten Seemann +[01:25:51] Obtained from https://github.com/tseemann/snippy +[01:25:51] Detected operating system: linux +[01:25:51] Enabling bundled linux tools. +[01:25:51] Found bwa - /usr/bin/bwa +[01:25:51] Found bcftools - /usr/bin/bcftools +[01:25:51] Found samtools - /usr/bin/samtools +[01:25:52] Found java - /usr/bin/java +[01:25:52] Found snpEff - /usr/bin/snpEff +[01:25:52] Found samclip - /usr/bin/samclip +[01:25:52] Found seqtk - /usr/bin/seqtk +[01:25:52] Found parallel - /usr/bin/parallel +[01:25:52] Found freebayes - /usr/bin/freebayes +[01:25:52] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[01:25:52] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[01:25:52] Found vcfstreamsort - /usr/bin/vcfstreamsort +[01:25:52] Found vcfuniq - /usr/bin/vcfuniq +[01:25:52] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[01:25:52] Found gzip - /usr/bin/gzip +[01:25:52] Found vt - /usr/bin/vt +[01:25:52] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[01:25:52] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[01:25:52] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[01:25:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[01:25:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[01:25:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[01:25:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[01:25:52] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[01:25:52] Treating reference as 'fasta' format. +[01:25:52] Will use 2 CPU cores. +[01:25:52] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq +[01:25:52] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[01:25:52] Used --force, will overwrite existing S3 +[01:25:52] Changing working directory: S3 +[01:25:52] Creating reference folder: reference +[01:25:52] Extracting FASTA and GFF from reference. +[01:25:52] Wrote 3 sequences to ref.fa +[01:25:52] Wrote 0 features to ref.gff +[01:25:52] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[01:25:52] Using BAM RG (Read Group) ID: S3 +[01:25:52] Running: samtools faidx reference/ref.fa 2>> snps.log +[01:25:52] Running: bwa index reference/ref.fa 2>> snps.log +[01:25:52] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[01:25:52] Running: ln -sf reference/ref.fa . 2>> snps.log +[01:25:52] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[01:25:52] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[01:25:52] 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) @@ -2840,17 +2876,17 @@ [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 2.305 CPU sec, 2.406 real sec -[samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 +[M::mem_process_seqs] Processed 24000 reads in 1.384 CPU sec, 0.697 real sec [main] Version: 0.7.19-r1273 -[main] CMD: bwa[samclip] Header contained 6 lines - mem -Y[samclip] Done. - -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: 2.782 sec; CPU: 2.376 sec -[05:42:45] Running: samtools index snps.bam 2>> snps.log -[05:42:45] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[05:42:45] 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 -[05:42:51] 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] 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: 0.826 sec; CPU: 1.436 sec +[samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 +[samclip] Header contained 6 lines +[samclip] Done. +[01:25:53] Running: samtools index snps.bam 2>> snps.log +[01:25:53] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[01:25:53] 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 +[01:25:54] 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 - @@ -2885,45 +2921,45 @@ total no. variants observed : 254 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[05:42:52] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[05:42:52] 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 -[05:42:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[05:42:52] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[05:42:52] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[05:42:52] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[05:42:52] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[05:42:52] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[05:42:52] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[05:42:53] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[05:42:53] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[05:42:53] Marked 846 heterozygous sites with 'n' -[05:42:53] Creating extra output files: BED GFF CSV TXT HTML -[05:42:53] Identified 254 variants. -[05:42:53] Result folder: S3 -[05:42:53] Result files: -[05:42:53] * S3/snps.aligned.fa -[05:42:53] * S3/snps.bam -[05:42:53] * S3/snps.bam.bai -[05:42:53] * S3/snps.bed -[05:42:53] * S3/snps.consensus.fa -[05:42:53] * S3/snps.consensus.subs.fa -[05:42:53] * S3/snps.csv -[05:42:53] * S3/snps.filt.vcf -[05:42:53] * S3/snps.gff -[05:42:53] * S3/snps.html -[05:42:53] * S3/snps.log -[05:42:53] * S3/snps.raw.vcf -[05:42:53] * S3/snps.subs.vcf -[05:42:53] * S3/snps.tab -[05:42:53] * S3/snps.txt -[05:42:53] * S3/snps.vcf -[05:42:53] * S3/snps.vcf.gz -[05:42:53] * S3/snps.vcf.gz.csi -[05:42:53] Walltime used: 16 seconds -[05:42:53] Questionable SNP? Try the --report option to see the alignments. -[05:42:53] Done. +[01:25:54] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[01:25:54] 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 +[01:25:54] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[01:25:54] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[01:25:54] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[01:25:55] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[01:25:55] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[01:25:55] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[01:25:55] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[01:25:55] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[01:25:55] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[01:25:55] Marked 846 heterozygous sites with 'n' +[01:25:55] Creating extra output files: BED GFF CSV TXT HTML +[01:25:55] Identified 254 variants. +[01:25:55] Result folder: S3 +[01:25:55] Result files: +[01:25:55] * S3/snps.aligned.fa +[01:25:55] * S3/snps.bam +[01:25:55] * S3/snps.bam.bai +[01:25:55] * S3/snps.bed +[01:25:55] * S3/snps.consensus.fa +[01:25:55] * S3/snps.consensus.subs.fa +[01:25:55] * S3/snps.csv +[01:25:55] * S3/snps.filt.vcf +[01:25:55] * S3/snps.gff +[01:25:55] * S3/snps.html +[01:25:55] * S3/snps.log +[01:25:55] * S3/snps.raw.vcf +[01:25:55] * S3/snps.subs.vcf +[01:25:55] * S3/snps.tab +[01:25:55] * S3/snps.txt +[01:25:55] * S3/snps.vcf +[01:25:55] * S3/snps.vcf.gz +[01:25:55] * S3/snps.vcf.gz.csi +[01:25:55] Walltime used: 4 seconds +[01:25:55] May the SNPs be with you. +[01:25:55] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2932,54 +2968,54 @@ [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 S4 --R1 S4/R1.fq --R2 S4/R2.fq -[05:42:54] This is snippy 4.6.0 -[05:42:54] Written by Torsten Seemann -[05:42:54] Obtained from https://github.com/tseemann/snippy -[05:42:54] Detected operating system: linux -[05:42:54] Enabling bundled linux tools. -[05:42:54] Found bwa - /usr/bin/bwa -[05:42:54] Found bcftools - /usr/bin/bcftools -[05:42:54] Found samtools - /usr/bin/samtools -[05:42:54] Found java - /usr/bin/java -[05:42:54] Found snpEff - /usr/bin/snpEff -[05:42:54] Found samclip - /usr/bin/samclip -[05:42:54] Found seqtk - /usr/bin/seqtk -[05:42:54] Found parallel - /usr/bin/parallel -[05:42:54] Found freebayes - /usr/bin/freebayes -[05:42:54] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[05:42:54] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[05:42:54] Found vcfstreamsort - /usr/bin/vcfstreamsort -[05:42:54] Found vcfuniq - /usr/bin/vcfuniq -[05:42:54] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[05:42:54] Found gzip - /usr/bin/gzip -[05:42:54] Found vt - /usr/bin/vt -[05:42:54] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[05:42:54] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[05:42:54] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[05:42:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[05:42:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[05:42:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[05:42:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[05:42:55] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[05:42:55] Treating reference as 'fasta' format. -[05:42:55] Will use 2 CPU cores. -[05:42:55] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq -[05:42:55] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[05:42:55] Used --force, will overwrite existing S4 -[05:42:55] Changing working directory: S4 -[05:42:55] Creating reference folder: reference -[05:42:55] Extracting FASTA and GFF from reference. -[05:42:55] Wrote 3 sequences to ref.fa -[05:42:55] Wrote 0 features to ref.gff -[05:42:55] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[05:42:55] Using BAM RG (Read Group) ID: S4 -[05:42:55] Running: samtools faidx reference/ref.fa 2>> snps.log -[05:42:55] Running: bwa index reference/ref.fa 2>> snps.log -[05:42:55] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[05:42:55] Running: ln -sf reference/ref.fa . 2>> snps.log -[05:42:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[05:42:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[05:42:55] 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 +[01:25:55] This is snippy 4.6.0 +[01:25:55] Written by Torsten Seemann +[01:25:55] Obtained from https://github.com/tseemann/snippy +[01:25:55] Detected operating system: linux +[01:25:55] Enabling bundled linux tools. +[01:25:55] Found bwa - /usr/bin/bwa +[01:25:55] Found bcftools - /usr/bin/bcftools +[01:25:55] Found samtools - /usr/bin/samtools +[01:25:55] Found java - /usr/bin/java +[01:25:55] Found snpEff - /usr/bin/snpEff +[01:25:55] Found samclip - /usr/bin/samclip +[01:25:55] Found seqtk - /usr/bin/seqtk +[01:25:55] Found parallel - /usr/bin/parallel +[01:25:55] Found freebayes - /usr/bin/freebayes +[01:25:55] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[01:25:55] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[01:25:55] Found vcfstreamsort - /usr/bin/vcfstreamsort +[01:25:55] Found vcfuniq - /usr/bin/vcfuniq +[01:25:55] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[01:25:55] Found gzip - /usr/bin/gzip +[01:25:55] Found vt - /usr/bin/vt +[01:25:55] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[01:25:55] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[01:25:55] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[01:25:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[01:25:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[01:25:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[01:25:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[01:25:55] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[01:25:55] Treating reference as 'fasta' format. +[01:25:55] Will use 2 CPU cores. +[01:25:55] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq +[01:25:55] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[01:25:55] Used --force, will overwrite existing S4 +[01:25:55] Changing working directory: S4 +[01:25:55] Creating reference folder: reference +[01:25:55] Extracting FASTA and GFF from reference. +[01:25:55] Wrote 3 sequences to ref.fa +[01:25:55] Wrote 0 features to ref.gff +[01:25:55] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[01:25:55] Using BAM RG (Read Group) ID: S4 +[01:25:55] Running: samtools faidx reference/ref.fa 2>> snps.log +[01:25:55] Running: bwa index reference/ref.fa 2>> snps.log +[01:25:55] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[01:25:55] Running: ln -sf reference/ref.fa . 2>> snps.log +[01:25:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[01:25:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[01:25:55] 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) @@ -2994,17 +3030,17 @@ [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 4.265 CPU sec, 3.680 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.361 CPU sec, 0.684 real sec [main] Version: 0.7.19-r1273 -[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: 4.083 sec; CPU: 4.344 sec -[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 -[samclip] Header contained 6 lines +[main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa[samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 + /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] Header contained 6 lines [samclip] Done. -[05:43:01] Running: samtools index snps.bam 2>> snps.log -[05:43:01] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[05:43:01] 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 -[05:43:04] 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: 0.807 sec; CPU: 1.408 sec +[01:25:56] Running: samtools index snps.bam 2>> snps.log +[01:25:56] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[01:25:57] 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 +[01:25:58] 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 - @@ -3039,45 +3075,45 @@ total no. variants observed : 257 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[05:43:04] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[05:43:04] 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 -[05:43:04] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[05:43:04] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[05:43:05] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[05:43:05] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[05:43:05] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[05:43:05] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[05:43:05] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[05:43:05] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[05:43:05] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[05:43:06] Marked 799 heterozygous sites with 'n' -[05:43:06] Creating extra output files: BED GFF CSV TXT HTML -[05:43:06] Identified 257 variants. -[05:43:06] Result folder: S4 -[05:43:06] Result files: -[05:43:06] * S4/snps.aligned.fa -[05:43:06] * S4/snps.bam -[05:43:06] * S4/snps.bam.bai -[05:43:06] * S4/snps.bed -[05:43:06] * S4/snps.consensus.fa -[05:43:06] * S4/snps.consensus.subs.fa -[05:43:06] * S4/snps.csv -[05:43:06] * S4/snps.filt.vcf -[05:43:06] * S4/snps.gff -[05:43:06] * S4/snps.html -[05:43:06] * S4/snps.log -[05:43:06] * S4/snps.raw.vcf -[05:43:06] * S4/snps.subs.vcf -[05:43:06] * S4/snps.tab -[05:43:06] * S4/snps.txt -[05:43:06] * S4/snps.vcf -[05:43:06] * S4/snps.vcf.gz -[05:43:06] * S4/snps.vcf.gz.csi -[05:43:06] Walltime used: 12 seconds -[05:43:06] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md -[05:43:06] Done. +[01:25:58] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[01:25:58] 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 +[01:25:58] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[01:25:58] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[01:25:58] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[01:25:58] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[01:25:58] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[01:25:58] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[01:25:58] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[01:25:58] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[01:25:58] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[01:26:00] Marked 799 heterozygous sites with 'n' +[01:26:00] Creating extra output files: BED GFF CSV TXT HTML +[01:26:00] Identified 257 variants. +[01:26:00] Result folder: S4 +[01:26:00] Result files: +[01:26:00] * S4/snps.aligned.fa +[01:26:00] * S4/snps.bam +[01:26:00] * S4/snps.bam.bai +[01:26:00] * S4/snps.bed +[01:26:00] * S4/snps.consensus.fa +[01:26:00] * S4/snps.consensus.subs.fa +[01:26:00] * S4/snps.csv +[01:26:00] * S4/snps.filt.vcf +[01:26:00] * S4/snps.gff +[01:26:00] * S4/snps.html +[01:26:00] * S4/snps.log +[01:26:00] * S4/snps.raw.vcf +[01:26:00] * S4/snps.subs.vcf +[01:26:00] * S4/snps.tab +[01:26:00] * S4/snps.txt +[01:26:00] * S4/snps.vcf +[01:26:00] * S4/snps.vcf.gz +[01:26:00] * S4/snps.vcf.gz.csi +[01:26:00] Walltime used: 5 seconds +[01:26:00] May the SNPs be with you. +[01:26:00] 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 @@ -3110,7 +3146,7 @@ Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln -The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md +This analysis is totally hard-core! Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy @@ -3144,7 +3180,7 @@ Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln -Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues +The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md Done. wc -l S?/snps.tab 262 S1/snps.tab @@ -3173,8 +3209,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-5_all.deb'. dpkg-deb: building package 'snippy' in '../snippy_4.6.0+dfsg-5_all.deb'. +dpkg-deb: building package 'snippy-examples' in '../snippy-examples_4.6.0+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../snippy_4.6.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../snippy_4.6.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3182,12 +3218,14 @@ 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/1551041/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1551041/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/3313594 and its subdirectories -I: Current time: Wed Oct 14 05:43:35 -12 2026 -I: pbuilder-time-stamp: 1791999815 +I: removing directory /srv/workspace/pbuilder/1551041 and its subdirectories +I: Current time: Fri Sep 12 01:26:07 +14 2025 +I: pbuilder-time-stamp: 1757589967