Diff of the two buildlogs: -- --- b1/build.log 2025-01-31 07:09:10.541097254 +0000 +++ b2/build.log 2025-01-31 07:11:23.163123438 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 30 19:01:20 -12 2025 -I: pbuilder-time-stamp: 1738306880 +I: Current time: Fri Mar 6 03:32:11 +14 2026 +I: pbuilder-time-stamp: 1772717531 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ 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/1848573/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1068398/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Mar 5 13:32 /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/1068398/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1068398/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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='a85b220b177642f1a0f8ec26ac1b60b7' - 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='1848573' - PS1='# ' - PS2='> ' + INVOCATION_ID=7323996a47244d8f81f3d07bd95d4749 + 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=1068398 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.itNRDS9z/pbuilderrc_NidX --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.itNRDS9z/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.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.itNRDS9z/pbuilderrc_yQD0 --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.itNRDS9z/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1848573/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1068398/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -556,7 +588,7 @@ Get: 416 http://deb.debian.org/debian unstable/main amd64 snp-sites amd64 2.5.1-2+b2 [13.9 kB] Get: 417 http://deb.debian.org/debian unstable/main amd64 snpeff all 5.2.e+dfsg-1 [7200 B] Get: 418 http://deb.debian.org/debian unstable/main amd64 vt amd64 0.57721+ds-3+b1 [841 kB] -Fetched 325 MB in 12s (26.5 MB/s) +Fetched 325 MB in 9s (37.3 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 ... 19842 files and directories currently installed.) @@ -1931,8 +1963,8 @@ Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 31 07:06:04 UTC 2025. -Universal Time is now: Fri Jan 31 07:06:04 UTC 2025. +Local time is now: Thu Mar 5 13:33:29 UTC 2026. +Universal Time is now: Thu Mar 5 13:33:29 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2460,7 +2492,11 @@ 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/1068398/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1068398/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 @@ -2486,59 +2522,59 @@ [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 -[19:07:46] This is snippy 4.6.0 -[19:07:46] Written by Torsten Seemann -[19:07:46] Obtained from https://github.com/tseemann/snippy -[19:07:46] Detected operating system: linux -[19:07:46] Enabling bundled linux tools. -[19:07:46] Found bwa - /usr/bin/bwa -[19:07:46] Found bcftools - /usr/bin/bcftools -[19:07:46] Found samtools - /usr/bin/samtools -[19:07:46] Found java - /usr/bin/java -[19:07:46] Found snpEff - /usr/bin/snpEff -[19:07:46] Found samclip - /usr/bin/samclip -[19:07:46] Found seqtk - /usr/bin/seqtk -[19:07:46] Found parallel - /usr/bin/parallel -[19:07:46] Found freebayes - /usr/bin/freebayes -[19:07:46] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[19:07:46] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[19:07:46] Found vcfstreamsort - /usr/bin/vcfstreamsort -[19:07:46] Found vcfuniq - /usr/bin/vcfuniq -[19:07:46] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[19:07:46] Found gzip - /usr/bin/gzip -[19:07:46] Found vt - /usr/bin/vt -[19:07:46] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[19:07:46] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[19:07:46] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[19:07:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[19:07:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[19:07:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[19:07:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[19:07:47] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[19:07:47] Treating reference as 'fasta' format. -[19:07:47] Will use 2 CPU cores. -[19:07:47] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq -[19:07:47] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[19:07:47] Used --force, will overwrite existing S1 -[19:07:47] Changing working directory: S1 -[19:07:47] Creating reference folder: reference -[19:07:47] Extracting FASTA and GFF from reference. -[19:07:48] Wrote 3 sequences to ref.fa -[19:07:48] Wrote 0 features to ref.gff -[19:07:48] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[19:07:48] Using BAM RG (Read Group) ID: S1 -[19:07:48] Running: samtools faidx reference/ref.fa 2>> snps.log -[19:07:48] Running: bwa index reference/ref.fa 2>> snps.log -[19:07:48] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[19:07:48] Running: ln -sf reference/ref.fa . 2>> snps.log -[19:07:48] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[19:07:48] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[19:07:48] 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 +[03:34:00] This is snippy 4.6.0 +[03:34:00] Written by Torsten Seemann +[03:34:00] Obtained from https://github.com/tseemann/snippy +[03:34:00] Detected operating system: linux +[03:34:00] Enabling bundled linux tools. +[03:34:00] Found bwa - /usr/bin/bwa +[03:34:00] Found bcftools - /usr/bin/bcftools +[03:34:00] Found samtools - /usr/bin/samtools +[03:34:00] Found java - /usr/bin/java +[03:34:00] Found snpEff - /usr/bin/snpEff +[03:34:00] Found samclip - /usr/bin/samclip +[03:34:00] Found seqtk - /usr/bin/seqtk +[03:34:00] Found parallel - /usr/bin/parallel +[03:34:00] Found freebayes - /usr/bin/freebayes +[03:34:00] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[03:34:00] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[03:34:00] Found vcfstreamsort - /usr/bin/vcfstreamsort +[03:34:00] Found vcfuniq - /usr/bin/vcfuniq +[03:34:00] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[03:34:00] Found gzip - /usr/bin/gzip +[03:34:00] Found vt - /usr/bin/vt +[03:34:00] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[03:34:00] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[03:34:00] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[03:34:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[03:34:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[03:34:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[03:34:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[03:34:00] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[03:34:00] Treating reference as 'fasta' format. +[03:34:00] Will use 2 CPU cores. +[03:34:00] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq +[03:34:00] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[03:34:00] Used --force, will overwrite existing S1 +[03:34:00] Changing working directory: S1 +[03:34:00] Creating reference folder: reference +[03:34:00] Extracting FASTA and GFF from reference. +[03:34:00] Wrote 3 sequences to ref.fa +[03:34:00] Wrote 0 features to ref.gff +[03:34:00] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[03:34:00] Using BAM RG (Read Group) ID: S1 +[03:34:00] Running: samtools faidx reference/ref.fa 2>> snps.log +[03:34:00] Running: bwa index reference/ref.fa 2>> snps.log +[03:34:01] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[03:34:01] Running: ln -sf reference/ref.fa . 2>> snps.log +[03:34:01] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[03:34:01] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[03:34:01] 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) [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, 11587, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... @@ -2548,17 +2584,17 @@ [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 2.404 CPU sec, 1.751 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.393 CPU sec, 0.702 real sec [main] Version: 0.7.18-r1243-dirty [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: 2.428 sec; CPU: 2.496 sec +[main] Real time: 0.797 sec; CPU: 1.439 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. -[19:07:52] Running: samtools index snps.bam 2>> snps.log -[19:07:52] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[19:07:53] 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 -[19:07:58] 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 +[03:34:02] Running: samtools index snps.bam 2>> snps.log +[03:34:02] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[03:34:02] 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 +[03:34:03] 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 - @@ -2593,45 +2629,45 @@ total no. variants observed : 261 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[19:07:58] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[19:07:58] 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 -[19:07:58] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[19:07:59] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[19:07:59] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[19:07:59] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[19:07:59] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[19:07:59] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[19:07:59] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[19:07:59] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[19:07:59] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[19:08:00] Marked 749 heterozygous sites with 'n' -[19:08:00] Creating extra output files: BED GFF CSV TXT HTML -[19:08:00] Identified 261 variants. -[19:08:00] Result folder: S1 -[19:08:00] Result files: -[19:08:00] * S1/snps.aligned.fa -[19:08:00] * S1/snps.bam -[19:08:00] * S1/snps.bam.bai -[19:08:00] * S1/snps.bed -[19:08:00] * S1/snps.consensus.fa -[19:08:00] * S1/snps.consensus.subs.fa -[19:08:00] * S1/snps.csv -[19:08:00] * S1/snps.filt.vcf -[19:08:00] * S1/snps.gff -[19:08:00] * S1/snps.html -[19:08:00] * S1/snps.log -[19:08:00] * S1/snps.raw.vcf -[19:08:00] * S1/snps.subs.vcf -[19:08:00] * S1/snps.tab -[19:08:00] * S1/snps.txt -[19:08:00] * S1/snps.vcf -[19:08:00] * S1/snps.vcf.gz -[19:08:00] * S1/snps.vcf.gz.csi -[19:08:00] Walltime used: 14 seconds -[19:08:00] May the SNPs be with you. -[19:08:00] Done. +[03:34:03] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[03:34:03] 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 +[03:34:03] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[03:34:03] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[03:34:03] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[03:34:03] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[03:34:03] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[03:34:03] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[03:34:03] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[03:34:03] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[03:34:03] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[03:34:04] Marked 749 heterozygous sites with 'n' +[03:34:04] Creating extra output files: BED GFF CSV TXT HTML +[03:34:04] Identified 261 variants. +[03:34:04] Result folder: S1 +[03:34:04] Result files: +[03:34:04] * S1/snps.aligned.fa +[03:34:04] * S1/snps.bam +[03:34:04] * S1/snps.bam.bai +[03:34:04] * S1/snps.bed +[03:34:04] * S1/snps.consensus.fa +[03:34:04] * S1/snps.consensus.subs.fa +[03:34:04] * S1/snps.csv +[03:34:04] * S1/snps.filt.vcf +[03:34:04] * S1/snps.gff +[03:34:04] * S1/snps.html +[03:34:04] * S1/snps.log +[03:34:04] * S1/snps.raw.vcf +[03:34:04] * S1/snps.subs.vcf +[03:34:04] * S1/snps.tab +[03:34:04] * S1/snps.txt +[03:34:04] * S1/snps.vcf +[03:34:04] * S1/snps.vcf.gz +[03:34:04] * S1/snps.vcf.gz.csi +[03:34:04] Walltime used: 4 seconds +[03:34:04] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md +[03:34:04] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2640,54 +2676,54 @@ [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 -[19:08:01] This is snippy 4.6.0 -[19:08:01] Written by Torsten Seemann -[19:08:01] Obtained from https://github.com/tseemann/snippy -[19:08:01] Detected operating system: linux -[19:08:01] Enabling bundled linux tools. -[19:08:01] Found bwa - /usr/bin/bwa -[19:08:01] Found bcftools - /usr/bin/bcftools -[19:08:01] Found samtools - /usr/bin/samtools -[19:08:01] Found java - /usr/bin/java -[19:08:01] Found snpEff - /usr/bin/snpEff -[19:08:01] Found samclip - /usr/bin/samclip -[19:08:01] Found seqtk - /usr/bin/seqtk -[19:08:01] Found parallel - /usr/bin/parallel -[19:08:01] Found freebayes - /usr/bin/freebayes -[19:08:01] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[19:08:01] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[19:08:01] Found vcfstreamsort - /usr/bin/vcfstreamsort -[19:08:01] Found vcfuniq - /usr/bin/vcfuniq -[19:08:01] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[19:08:01] Found gzip - /usr/bin/gzip -[19:08:01] Found vt - /usr/bin/vt -[19:08:01] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[19:08:01] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[19:08:02] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[19:08:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[19:08:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[19:08:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[19:08:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[19:08:03] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[19:08:03] Treating reference as 'fasta' format. -[19:08:03] Will use 2 CPU cores. -[19:08:03] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq -[19:08:03] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[19:08:03] Used --force, will overwrite existing S2 -[19:08:03] Changing working directory: S2 -[19:08:03] Creating reference folder: reference -[19:08:03] Extracting FASTA and GFF from reference. -[19:08:03] Wrote 3 sequences to ref.fa -[19:08:03] Wrote 0 features to ref.gff -[19:08:03] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[19:08:03] Using BAM RG (Read Group) ID: S2 -[19:08:03] Running: samtools faidx reference/ref.fa 2>> snps.log -[19:08:03] Running: bwa index reference/ref.fa 2>> snps.log -[19:08:03] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[19:08:03] Running: ln -sf reference/ref.fa . 2>> snps.log -[19:08:03] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[19:08:03] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[19:08:03] 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 +[03:34:04] This is snippy 4.6.0 +[03:34:04] Written by Torsten Seemann +[03:34:04] Obtained from https://github.com/tseemann/snippy +[03:34:04] Detected operating system: linux +[03:34:04] Enabling bundled linux tools. +[03:34:04] Found bwa - /usr/bin/bwa +[03:34:04] Found bcftools - /usr/bin/bcftools +[03:34:04] Found samtools - /usr/bin/samtools +[03:34:04] Found java - /usr/bin/java +[03:34:04] Found snpEff - /usr/bin/snpEff +[03:34:04] Found samclip - /usr/bin/samclip +[03:34:04] Found seqtk - /usr/bin/seqtk +[03:34:04] Found parallel - /usr/bin/parallel +[03:34:04] Found freebayes - /usr/bin/freebayes +[03:34:04] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[03:34:04] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[03:34:04] Found vcfstreamsort - /usr/bin/vcfstreamsort +[03:34:04] Found vcfuniq - /usr/bin/vcfuniq +[03:34:04] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[03:34:04] Found gzip - /usr/bin/gzip +[03:34:04] Found vt - /usr/bin/vt +[03:34:04] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[03:34:04] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[03:34:04] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[03:34:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[03:34:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[03:34:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[03:34:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[03:34:04] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[03:34:04] Treating reference as 'fasta' format. +[03:34:04] Will use 2 CPU cores. +[03:34:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq +[03:34:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq +[03:34:04] Used --force, will overwrite existing S2 +[03:34:04] Changing working directory: S2 +[03:34:04] Creating reference folder: reference +[03:34:04] Extracting FASTA and GFF from reference. +[03:34:04] Wrote 3 sequences to ref.fa +[03:34:04] Wrote 0 features to ref.gff +[03:34:04] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[03:34:04] Using BAM RG (Read Group) ID: S2 +[03:34:04] Running: samtools faidx reference/ref.fa 2>> snps.log +[03:34:04] Running: bwa index reference/ref.fa 2>> snps.log +[03:34:04] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[03:34:04] Running: ln -sf reference/ref.fa . 2>> snps.log +[03:34:04] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[03:34:04] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[03:34:04] 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) @@ -2702,17 +2738,17 @@ [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 2.485 CPU sec, 1.975 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.425 CPU sec, 0.719 real sec [main] Version: 0.7.18-r1243-dirty [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: 2.999 sec; CPU: 2.592 sec +[main] Real time: 0.839 sec; CPU: 1.472 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. -[19:08:08] Running: samtools index snps.bam 2>> snps.log -[19:08:08] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[19:08:08] 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 -[19:08:13] 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 +[03:34:05] Running: samtools index snps.bam 2>> snps.log +[03:34:05] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[03:34:05] 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 +[03:34:06] 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 - @@ -2747,45 +2783,45 @@ total no. variants observed : 246 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[19:08:13] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[19:08:13] 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 -[19:08:13] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[19:08:14] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[19:08:14] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[19:08:14] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[19:08:14] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[19:08:14] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[19:08:14] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[19:08:14] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[19:08:14] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[19:08:15] Marked 841 heterozygous sites with 'n' -[19:08:15] Creating extra output files: BED GFF CSV TXT HTML -[19:08:15] Identified 246 variants. -[19:08:15] Result folder: S2 -[19:08:15] Result files: -[19:08:15] * S2/snps.aligned.fa -[19:08:15] * S2/snps.bam -[19:08:15] * S2/snps.bam.bai -[19:08:15] * S2/snps.bed -[19:08:15] * S2/snps.consensus.fa -[19:08:15] * S2/snps.consensus.subs.fa -[19:08:15] * S2/snps.csv -[19:08:15] * S2/snps.filt.vcf -[19:08:15] * S2/snps.gff -[19:08:15] * S2/snps.html -[19:08:15] * S2/snps.log -[19:08:15] * S2/snps.raw.vcf -[19:08:15] * S2/snps.subs.vcf -[19:08:15] * S2/snps.tab -[19:08:15] * S2/snps.txt -[19:08:15] * S2/snps.vcf -[19:08:15] * S2/snps.vcf.gz -[19:08:15] * S2/snps.vcf.gz.csi -[19:08:15] Walltime used: 14 seconds -[19:08:15] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues -[19:08:15] Done. +[03:34:06] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[03:34:06] 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 +[03:34:07] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[03:34:07] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[03:34:07] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[03:34:07] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[03:34:07] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[03:34:07] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[03:34:07] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[03:34:07] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[03:34:07] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[03:34:07] Marked 841 heterozygous sites with 'n' +[03:34:07] Creating extra output files: BED GFF CSV TXT HTML +[03:34:07] Identified 246 variants. +[03:34:07] Result folder: S2 +[03:34:07] Result files: +[03:34:07] * S2/snps.aligned.fa +[03:34:07] * S2/snps.bam +[03:34:07] * S2/snps.bam.bai +[03:34:07] * S2/snps.bed +[03:34:07] * S2/snps.consensus.fa +[03:34:07] * S2/snps.consensus.subs.fa +[03:34:07] * S2/snps.csv +[03:34:07] * S2/snps.filt.vcf +[03:34:07] * S2/snps.gff +[03:34:07] * S2/snps.html +[03:34:07] * S2/snps.log +[03:34:07] * S2/snps.raw.vcf +[03:34:07] * S2/snps.subs.vcf +[03:34:07] * S2/snps.tab +[03:34:07] * S2/snps.txt +[03:34:07] * S2/snps.vcf +[03:34:07] * S2/snps.vcf.gz +[03:34:07] * S2/snps.vcf.gz.csi +[03:34:07] Walltime used: 3 seconds +[03:34:07] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md +[03:34:07] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2794,59 +2830,59 @@ [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 -[19:08:16] This is snippy 4.6.0 -[19:08:16] Written by Torsten Seemann -[19:08:16] Obtained from https://github.com/tseemann/snippy -[19:08:16] Detected operating system: linux -[19:08:16] Enabling bundled linux tools. -[19:08:16] Found bwa - /usr/bin/bwa -[19:08:16] Found bcftools - /usr/bin/bcftools -[19:08:16] Found samtools - /usr/bin/samtools -[19:08:16] Found java - /usr/bin/java -[19:08:16] Found snpEff - /usr/bin/snpEff -[19:08:16] Found samclip - /usr/bin/samclip -[19:08:16] Found seqtk - /usr/bin/seqtk -[19:08:16] Found parallel - /usr/bin/parallel -[19:08:16] Found freebayes - /usr/bin/freebayes -[19:08:16] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[19:08:16] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[19:08:16] Found vcfstreamsort - /usr/bin/vcfstreamsort -[19:08:16] Found vcfuniq - /usr/bin/vcfuniq -[19:08:17] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[19:08:17] Found gzip - /usr/bin/gzip -[19:08:17] Found vt - /usr/bin/vt -[19:08:17] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[19:08:17] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[19:08:17] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[19:08:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[19:08:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[19:08:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[19:08:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[19:08:18] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[19:08:18] Treating reference as 'fasta' format. -[19:08:18] Will use 2 CPU cores. -[19:08:18] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq -[19:08:18] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[19:08:18] Used --force, will overwrite existing S3 -[19:08:18] Changing working directory: S3 -[19:08:18] Creating reference folder: reference -[19:08:18] Extracting FASTA and GFF from reference. -[19:08:18] Wrote 3 sequences to ref.fa -[19:08:18] Wrote 0 features to ref.gff -[19:08:18] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[19:08:18] Using BAM RG (Read Group) ID: S3 -[19:08:18] Running: samtools faidx reference/ref.fa 2>> snps.log -[19:08:18] Running: bwa index reference/ref.fa 2>> snps.log -[19:08:18] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[19:08:18] Running: ln -sf reference/ref.fa . 2>> snps.log -[19:08:18] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[19:08:18] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[19:08:18] 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 +[03:34:07] This is snippy 4.6.0 +[03:34:07] Written by Torsten Seemann +[03:34:07] Obtained from https://github.com/tseemann/snippy +[03:34:07] Detected operating system: linux +[03:34:07] Enabling bundled linux tools. +[03:34:07] Found bwa - /usr/bin/bwa +[03:34:07] Found bcftools - /usr/bin/bcftools +[03:34:07] Found samtools - /usr/bin/samtools +[03:34:07] Found java - /usr/bin/java +[03:34:07] Found snpEff - /usr/bin/snpEff +[03:34:07] Found samclip - /usr/bin/samclip +[03:34:07] Found seqtk - /usr/bin/seqtk +[03:34:07] Found parallel - /usr/bin/parallel +[03:34:07] Found freebayes - /usr/bin/freebayes +[03:34:07] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[03:34:07] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[03:34:07] Found vcfstreamsort - /usr/bin/vcfstreamsort +[03:34:07] Found vcfuniq - /usr/bin/vcfuniq +[03:34:07] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[03:34:07] Found gzip - /usr/bin/gzip +[03:34:07] Found vt - /usr/bin/vt +[03:34:07] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[03:34:07] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[03:34:07] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[03:34:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[03:34:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[03:34:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[03:34:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[03:34:07] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[03:34:07] Treating reference as 'fasta' format. +[03:34:07] Will use 2 CPU cores. +[03:34:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq +[03:34:07] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[03:34:07] Used --force, will overwrite existing S3 +[03:34:07] Changing working directory: S3 +[03:34:07] Creating reference folder: reference +[03:34:07] Extracting FASTA and GFF from reference. +[03:34:07] Wrote 3 sequences to ref.fa +[03:34:07] Wrote 0 features to ref.gff +[03:34:07] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[03:34:07] Using BAM RG (Read Group) ID: S3 +[03:34:07] Running: samtools faidx reference/ref.fa 2>> snps.log +[03:34:07] Running: bwa index reference/ref.fa 2>> snps.log +[03:34:07] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[03:34:07] Running: ln -sf reference/ref.fa . 2>> snps.log +[03:34:07] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[03:34:07] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[03:34:07] 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... @@ -2856,17 +2892,17 @@ [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 2.633 CPU sec, 2.104 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.425 CPU sec, 0.718 real sec [main] Version: 0.7.18-r1243-dirty [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: 2.937 sec; CPU: 2.726 sec +[main] Real time: 0.840 sec; CPU: 1.468 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. -[19:08:23] Running: samtools index snps.bam 2>> snps.log -[19:08:23] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[19:08:23] 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 -[19:08:29] 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 +[03:34:09] Running: samtools index snps.bam 2>> snps.log +[03:34:09] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[03:34:09] 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 +[03:34:10] 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 - @@ -2903,43 +2939,43 @@ Time elapsed: 0.01s -[19:08:29] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[19:08:29] 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 -[19:08:29] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[19:08:30] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[19:08:30] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[19:08:30] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[19:08:30] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[19:08:30] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[19:08:30] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[19:08:30] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[19:08:30] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[19:08:32] Marked 846 heterozygous sites with 'n' -[19:08:32] Creating extra output files: BED GFF CSV TXT HTML -[19:08:32] Identified 254 variants. -[19:08:32] Result folder: S3 -[19:08:32] Result files: -[19:08:32] * S3/snps.aligned.fa -[19:08:32] * S3/snps.bam -[19:08:32] * S3/snps.bam.bai -[19:08:32] * S3/snps.bed -[19:08:32] * S3/snps.consensus.fa -[19:08:32] * S3/snps.consensus.subs.fa -[19:08:32] * S3/snps.csv -[19:08:32] * S3/snps.filt.vcf -[19:08:32] * S3/snps.gff -[19:08:32] * S3/snps.html -[19:08:32] * S3/snps.log -[19:08:32] * S3/snps.raw.vcf -[19:08:32] * S3/snps.subs.vcf -[19:08:32] * S3/snps.tab -[19:08:32] * S3/snps.txt -[19:08:32] * S3/snps.vcf -[19:08:32] * S3/snps.vcf.gz -[19:08:32] * S3/snps.vcf.gz.csi -[19:08:32] Walltime used: 16 seconds -[19:08:32] Did you know? Snippy is a combination of SNP, Skippy, and snappy. -[19:08:32] Done. +[03:34:10] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[03:34:10] 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 +[03:34:10] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[03:34:10] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[03:34:10] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[03:34:10] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[03:34:10] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[03:34:10] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[03:34:10] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[03:34:10] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[03:34:10] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[03:34:11] Marked 846 heterozygous sites with 'n' +[03:34:11] Creating extra output files: BED GFF CSV TXT HTML +[03:34:11] Identified 254 variants. +[03:34:11] Result folder: S3 +[03:34:11] Result files: +[03:34:11] * S3/snps.aligned.fa +[03:34:11] * S3/snps.bam +[03:34:11] * S3/snps.bam.bai +[03:34:11] * S3/snps.bed +[03:34:11] * S3/snps.consensus.fa +[03:34:11] * S3/snps.consensus.subs.fa +[03:34:11] * S3/snps.csv +[03:34:11] * S3/snps.filt.vcf +[03:34:11] * S3/snps.gff +[03:34:11] * S3/snps.html +[03:34:11] * S3/snps.log +[03:34:11] * S3/snps.raw.vcf +[03:34:11] * S3/snps.subs.vcf +[03:34:11] * S3/snps.tab +[03:34:11] * S3/snps.txt +[03:34:11] * S3/snps.vcf +[03:34:11] * S3/snps.vcf.gz +[03:34:11] * S3/snps.vcf.gz.csi +[03:34:11] Walltime used: 4 seconds +[03:34:11] Questionable SNP? Try the --report option to see the alignments. +[03:34:11] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2948,54 +2984,54 @@ [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 -[19:08:33] This is snippy 4.6.0 -[19:08:33] Written by Torsten Seemann -[19:08:33] Obtained from https://github.com/tseemann/snippy -[19:08:33] Detected operating system: linux -[19:08:33] Enabling bundled linux tools. -[19:08:33] Found bwa - /usr/bin/bwa -[19:08:33] Found bcftools - /usr/bin/bcftools -[19:08:33] Found samtools - /usr/bin/samtools -[19:08:33] Found java - /usr/bin/java -[19:08:33] Found snpEff - /usr/bin/snpEff -[19:08:33] Found samclip - /usr/bin/samclip -[19:08:33] Found seqtk - /usr/bin/seqtk -[19:08:33] Found parallel - /usr/bin/parallel -[19:08:33] Found freebayes - /usr/bin/freebayes -[19:08:33] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[19:08:33] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[19:08:33] Found vcfstreamsort - /usr/bin/vcfstreamsort -[19:08:33] Found vcfuniq - /usr/bin/vcfuniq -[19:08:33] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[19:08:33] Found gzip - /usr/bin/gzip -[19:08:33] Found vt - /usr/bin/vt -[19:08:33] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[19:08:33] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[19:08:33] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[19:08:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[19:08:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[19:08:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[19:08:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[19:08:34] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[19:08:34] Treating reference as 'fasta' format. -[19:08:34] Will use 2 CPU cores. -[19:08:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq -[19:08:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[19:08:34] Used --force, will overwrite existing S4 -[19:08:34] Changing working directory: S4 -[19:08:34] Creating reference folder: reference -[19:08:34] Extracting FASTA and GFF from reference. -[19:08:34] Wrote 3 sequences to ref.fa -[19:08:34] Wrote 0 features to ref.gff -[19:08:34] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[19:08:34] Using BAM RG (Read Group) ID: S4 -[19:08:34] Running: samtools faidx reference/ref.fa 2>> snps.log -[19:08:34] Running: bwa index reference/ref.fa 2>> snps.log -[19:08:35] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[19:08:35] Running: ln -sf reference/ref.fa . 2>> snps.log -[19:08:35] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[19:08:35] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[19:08:35] 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 +[03:34:11] This is snippy 4.6.0 +[03:34:11] Written by Torsten Seemann +[03:34:11] Obtained from https://github.com/tseemann/snippy +[03:34:11] Detected operating system: linux +[03:34:11] Enabling bundled linux tools. +[03:34:11] Found bwa - /usr/bin/bwa +[03:34:11] Found bcftools - /usr/bin/bcftools +[03:34:11] Found samtools - /usr/bin/samtools +[03:34:11] Found java - /usr/bin/java +[03:34:11] Found snpEff - /usr/bin/snpEff +[03:34:11] Found samclip - /usr/bin/samclip +[03:34:11] Found seqtk - /usr/bin/seqtk +[03:34:11] Found parallel - /usr/bin/parallel +[03:34:11] Found freebayes - /usr/bin/freebayes +[03:34:11] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[03:34:11] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[03:34:11] Found vcfstreamsort - /usr/bin/vcfstreamsort +[03:34:11] Found vcfuniq - /usr/bin/vcfuniq +[03:34:11] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[03:34:11] Found gzip - /usr/bin/gzip +[03:34:11] Found vt - /usr/bin/vt +[03:34:11] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[03:34:11] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[03:34:11] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[03:34:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[03:34:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[03:34:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[03:34:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[03:34:11] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[03:34:11] Treating reference as 'fasta' format. +[03:34:11] Will use 2 CPU cores. +[03:34:11] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq +[03:34:11] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[03:34:11] Used --force, will overwrite existing S4 +[03:34:11] Changing working directory: S4 +[03:34:11] Creating reference folder: reference +[03:34:11] Extracting FASTA and GFF from reference. +[03:34:11] Wrote 3 sequences to ref.fa +[03:34:11] Wrote 0 features to ref.gff +[03:34:11] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[03:34:11] Using BAM RG (Read Group) ID: S4 +[03:34:11] Running: samtools faidx reference/ref.fa 2>> snps.log +[03:34:11] Running: bwa index reference/ref.fa 2>> snps.log +[03:34:11] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[03:34:11] Running: ln -sf reference/ref.fa . 2>> snps.log +[03:34:11] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[03:34:11] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[03:34:11] 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) @@ -3010,17 +3046,17 @@ [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 2.753 CPU sec, 2.900 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.350 CPU sec, 0.682 real sec [main] Version: 0.7.18-r1243-dirty [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: 3.946 sec; CPU: 2.851 sec +[main] Real time: 0.762 sec; CPU: 1.389 sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. -[19:08:41] Running: samtools index snps.bam 2>> snps.log -[19:08:41] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[19:08:42] 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 -[19:08:47] 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 +[03:34:12] Running: samtools index snps.bam 2>> snps.log +[03:34:12] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[03:34:12] 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 +[03:34:13] 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 - @@ -3055,45 +3091,45 @@ total no. variants observed : 257 total no. reference observed : 0 -Time elapsed: 0.01s +Time elapsed: 0.00s -[19:08:47] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[19:08:47] 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 -[19:08:47] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[19:08:47] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[19:08:47] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[19:08:47] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[19:08:47] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[19:08:47] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[19:08:47] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[19:08:47] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[19:08:47] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[19:08:49] Marked 799 heterozygous sites with 'n' -[19:08:49] Creating extra output files: BED GFF CSV TXT HTML -[19:08:49] Identified 257 variants. -[19:08:49] Result folder: S4 -[19:08:49] Result files: -[19:08:49] * S4/snps.aligned.fa -[19:08:49] * S4/snps.bam -[19:08:49] * S4/snps.bam.bai -[19:08:49] * S4/snps.bed -[19:08:49] * S4/snps.consensus.fa -[19:08:49] * S4/snps.consensus.subs.fa -[19:08:49] * S4/snps.csv -[19:08:49] * S4/snps.filt.vcf -[19:08:49] * S4/snps.gff -[19:08:49] * S4/snps.html -[19:08:49] * S4/snps.log -[19:08:49] * S4/snps.raw.vcf -[19:08:49] * S4/snps.subs.vcf -[19:08:49] * S4/snps.tab -[19:08:49] * S4/snps.txt -[19:08:49] * S4/snps.vcf -[19:08:49] * S4/snps.vcf.gz -[19:08:49] * S4/snps.vcf.gz.csi -[19:08:49] Walltime used: 16 seconds -[19:08:49] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues -[19:08:49] Done. +[03:34:14] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[03:34:14] 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 +[03:34:14] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[03:34:14] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[03:34:14] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[03:34:15] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[03:34:15] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[03:34:15] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[03:34:16] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[03:34:16] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[03:34:16] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[03:34:16] Marked 799 heterozygous sites with 'n' +[03:34:16] Creating extra output files: BED GFF CSV TXT HTML +[03:34:16] Identified 257 variants. +[03:34:16] Result folder: S4 +[03:34:16] Result files: +[03:34:16] * S4/snps.aligned.fa +[03:34:16] * S4/snps.bam +[03:34:16] * S4/snps.bam.bai +[03:34:16] * S4/snps.bed +[03:34:16] * S4/snps.consensus.fa +[03:34:16] * S4/snps.consensus.subs.fa +[03:34:16] * S4/snps.csv +[03:34:16] * S4/snps.filt.vcf +[03:34:16] * S4/snps.gff +[03:34:16] * S4/snps.html +[03:34:16] * S4/snps.log +[03:34:16] * S4/snps.raw.vcf +[03:34:16] * S4/snps.subs.vcf +[03:34:16] * S4/snps.tab +[03:34:16] * S4/snps.txt +[03:34:16] * S4/snps.vcf +[03:34:16] * S4/snps.vcf.gz +[03:34:16] * S4/snps.vcf.gz.csi +[03:34:16] Walltime used: 5 seconds +[03:34:16] Wishing you a life free of homopolymer errors. +[03:34:16] 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 @@ -3126,7 +3162,7 @@ Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln -Found a bug? Post it at http://github.com/tseemann/snippy/issues +Run 'snp-sites -b -c -o phylo.aln core.full.aln' for IQTree, BEAST, RaxML Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy @@ -3160,7 +3196,7 @@ Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln -This analysis is totally hard-core! +You can mask columns using '--mask BEDFILE --mask-char X' Done. wc -l S?/snps.tab 262 S1/snps.tab @@ -3189,8 +3225,8 @@ 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) @@ -3198,12 +3234,14 @@ 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/1068398/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1068398/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/1848573 and its subdirectories -I: Current time: Thu Jan 30 19:09:09 -12 2025 -I: pbuilder-time-stamp: 1738307349 +I: removing directory /srv/workspace/pbuilder/1068398 and its subdirectories +I: Current time: Fri Mar 6 03:34:21 +14 2026 +I: pbuilder-time-stamp: 1772717661