# HG changeset patch # User dfornika # Date 1552426649 14400 # Node ID 0e733df972b56009fe9cbb614b6f72fcc3fe2b5c # Parent 3bbfe41787afa97764412f5ec6b67566234ae869 planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty diff -r 3bbfe41787af -r 0e733df972b5 snippy.xml --- a/snippy.xml Fri Mar 08 20:46:56 2019 -0500 +++ b/snippy.xml Tue Mar 12 17:37:29 2019 -0400 @@ -30,7 +30,7 @@ --minfrac $adv.minfrac --minqual $adv.minqual #if $adv.rgid - --rgid '$advanced.rgid' + --rgid '$adv.rgid' #end if #if $adv.bwaopt --bwaopt '$advanced.bwaopt' @@ -56,12 +56,17 @@ #import re #if str( $fastq_input.fastq_input_selector ) == "paired" #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) #else #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier) #end if mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && tar -czf out.tgz ${dir_name} + #if "outcon" in str($outputs) and $adv.rename_cons + && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa + #end if ]]> @@ -99,6 +104,7 @@ + diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/ref.fa --- a/test-data/a/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/ref.fa.fai --- a/test-data/a/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/genomes/ref.fa --- a/test-data/a/reference/genomes/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.fa --- a/test-data/a/reference/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.fa.amb --- a/test-data/a/reference/ref.fa.amb Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -700 1 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.fa.ann --- a/test-data/a/reference/ref.fa.ann Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -700 1 11 -0 reference (null) -0 700 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.fa.bwt Binary file test-data/a/reference/ref.fa.bwt has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.fa.fai --- a/test-data/a/reference/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.fa.pac Binary file test-data/a/reference/ref.fa.pac has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.fa.sa Binary file test-data/a/reference/ref.fa.sa has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.gff diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref.txt --- a/test-data/a/reference/ref.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference:0-700 diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/reference/ref/genes.gff.gz Binary file test-data/a/reference/ref/genes.gff.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.aligned.fa --- a/test-data/a/snps.aligned.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------- diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.bam Binary file test-data/a/snps.bam has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.bam.bai Binary file test-data/a/snps.bam.bai has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.bed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.consensus.fa --- a/test-data/a/snps.consensus.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.consensus.subs.fa --- a/test-data/a/snps.consensus.subs.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.csv --- a/test-data/a/snps.csv Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,EFFECT,LOCUS_TAG,GENE,PRODUCT diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.filt.vcf --- a/test-data/a/snps.filt.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 11:34:57 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 11:34:57 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT a diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.gff --- a/test-data/a/snps.gff Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -##gff-version 3 diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.html --- a/test-data/a/snps.html Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - - -
CHROM -POS -TYPE -REF -ALT -EVIDENCE -FTYPE -STRAND -NT_POS -AA_POS -EFFECT -LOCUS_TAG -GENE -PRODUCT -
diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.log --- a/test-data/a/snps.log Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,348 +0,0 @@ -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.068 sec; CPU: 0.004 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.13194. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.13194. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.13194. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### 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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --force --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.14292. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14292. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14292. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 20 --force --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.15235. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.15235. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.15235. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=20 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.16998. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.16998. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.16998. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.raw.vcf --- a/test-data/a/snps.raw.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -##fileformat=VCFv4.2 -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT a diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.subs.vcf --- a/test-data/a/snps.subs.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -##fileformat=VCFv4.2 -##snippy="snippy-vcf_extract_subs snps.filt.vcf" -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 11:34:57 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 11:34:57 2019 -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT a diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.tab --- a/test-data/a/snps.tab Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS EFFECT LOCUS_TAG GENE PRODUCT diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.txt --- a/test-data/a/snps.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -DateTime 2019-02-06T11:34:56 -ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq -Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/reference.fasta -ReferenceSize 700 -Software snippy 4.3.6 -VariantTotal 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.vcf --- a/test-data/a/snps.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 11:34:57 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 11:34:57 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT a diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.vcf.gz Binary file test-data/a/snps.vcf.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/a/snps.vcf.gz.csi Binary file test-data/a/snps.vcf.gz.csi has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/ref.fa --- a/test-data/b/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/ref.fa.fai --- a/test-data/b/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/genomes/ref.fa --- a/test-data/b/reference/genomes/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.fa --- a/test-data/b/reference/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.fa.amb --- a/test-data/b/reference/ref.fa.amb Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -700 1 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.fa.ann --- a/test-data/b/reference/ref.fa.ann Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -700 1 11 -0 reference (null) -0 700 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.fa.bwt Binary file test-data/b/reference/ref.fa.bwt has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.fa.fai --- a/test-data/b/reference/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.fa.pac Binary file test-data/b/reference/ref.fa.pac has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.fa.sa Binary file test-data/b/reference/ref.fa.sa has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.gff diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref.txt --- a/test-data/b/reference/ref.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference:0-700 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/reference/ref/genes.gff.gz Binary file test-data/b/reference/ref/genes.gff.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.aligned.fa --- a/test-data/b/snps.aligned.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------- diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.bam Binary file test-data/b/snps.bam has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.bam.bai Binary file test-data/b/snps.bam.bai has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.bed --- a/test-data/b/snps.bed Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 3 4 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.consensus.fa --- a/test-data/b/snps.consensus.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.consensus.subs.fa --- a/test-data/b/snps.consensus.subs.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.csv --- a/test-data/b/snps.csv Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,EFFECT,LOCUS_TAG,GENE,PRODUCT -reference,4,snp,A,T,T:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.filt.vcf --- a/test-data/b/snps.filt.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:11:01 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:11:01 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b -reference 4 . A T 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.gff --- a/test-data/b/snps.gff Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -##gff-version 3 -reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.html --- a/test-data/b/snps.html Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ - - - -
CHROM -POS -TYPE -REF -ALT -EVIDENCE -FTYPE -STRAND -NT_POS -AA_POS -EFFECT -LOCUS_TAG -GENE -PRODUCT -
reference -4 -snp -A -T -T:2 A:0 -
diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.log --- a/test-data/b/snps.log Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,435 +0,0 @@ -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir b --ref reference.fasta --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.004 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.13430. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.13430. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.13430. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### 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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --force --outdir b --ref reference.fasta --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.14512. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14512. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14512. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 20 --force --outdir b --ref reference.fasta --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.15458. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.15458. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.15458. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=20 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 1 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b --ref reference.fasta --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.004 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.17221. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.17221. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.17221. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 1 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b --ref reference.fasta --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.23600. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.23600. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.23600. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 1 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.raw.vcf --- a/test-data/b/snps.raw.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -##fileformat=VCFv4.2 -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b -reference 4 . A T 63.8794 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.subs.vcf --- a/test-data/b/snps.subs.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -##fileformat=VCFv4.2 -##snippy="snippy-vcf_extract_subs snps.filt.vcf" -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:11:01 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:11:01 2019 -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b -reference 4 . A T 63.8794 . TYPE=snp;DP=2;RO=0;AO=2 GT:DP:RO:AO:QR:QA 1/1:2:0:2:0:80 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.tab --- a/test-data/b/snps.tab Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS EFFECT LOCUS_TAG GENE PRODUCT -reference 4 snp A T T:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.txt --- a/test-data/b/snps.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -DateTime 2019-02-06T12:11:00 -ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq -Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/reference.fasta -ReferenceSize 700 -Software snippy 4.3.6 -Variant-SNP 1 -VariantTotal 1 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.vcf --- a/test-data/b/snps.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:11:01 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:11:01 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b -reference 4 . A T 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.vcf.gz Binary file test-data/b/snps.vcf.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b/snps.vcf.gz.csi Binary file test-data/b/snps.vcf.gz.csi has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/ref.fa --- a/test-data/b_gbk/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference Listeria monocytogenes strain strain. -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/ref.fa.fai --- a/test-data/b_gbk/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 49 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/genomes/ref.fa --- a/test-data/b_gbk/reference/genomes/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference Listeria monocytogenes strain strain. -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.fa --- a/test-data/b_gbk/reference/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference Listeria monocytogenes strain strain. -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.fa.amb --- a/test-data/b_gbk/reference/ref.fa.amb Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -700 1 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.fa.ann --- a/test-data/b_gbk/reference/ref.fa.ann Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -700 1 11 -0 reference Listeria monocytogenes strain strain. -0 700 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.fa.bwt Binary file test-data/b_gbk/reference/ref.fa.bwt has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.fa.fai --- a/test-data/b_gbk/reference/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 49 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.fa.pac Binary file test-data/b_gbk/reference/ref.fa.pac has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.fa.sa Binary file test-data/b_gbk/reference/ref.fa.sa has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.gff --- a/test-data/b_gbk/reference/ref.gff Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -##gff-version 3 -reference snippy CDS 188 658 . + 0 ID=KPFNHDNB_00001;codon_start=1;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPFNHDNB_00001;product=hypothetical protein;transl_table=11;translation=MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref.txt --- a/test-data/b_gbk/reference/ref.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference:0-700 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref/genes.gff.gz Binary file test-data/b_gbk/reference/ref/genes.gff.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/ref/snpEffectPredictor.bin Binary file test-data/b_gbk/reference/ref/snpEffectPredictor.bin has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/reference/snpeff.config --- a/test-data/b_gbk/reference/snpeff.config Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -codon.Standard : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Vertebrate_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/*, AGG/*, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Yeast_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/T, CTC/T, CTA/T, CTG/T, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Mold_Mitochondrial : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Protozoan_Mitochondrial : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Coelenterate : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Mitochondrial : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Mycoplasma : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Spiroplasma : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Invertebrate_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Ciliate_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Dasycladacean_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Hexamita_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Echinoderm_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Flatworm_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Euplotid_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/C, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Bacterial_and_Plant_Plastid : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Alternative_Yeast_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Ascidian_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Alternative_Flatworm_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Blepharisma_Macronuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Chlorophycean_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Trematode_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Scenedesmus_obliquus_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Thraustochytrium_Mitochondrial : TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -ref.genome : Snippy Reference - ref.chromosome : reference - ref.reference.codonTable : Bacterial_and_Plant_Plastid diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/snps.bam Binary file test-data/b_gbk/snps.bam has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/snps.bam.bai Binary file test-data/b_gbk/snps.bam.bai has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/snps.filt.vcf --- a/test-data/b_gbk/snps.filt.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:11:38 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:11:38 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b_gbk -reference 4 . A T 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/snps.log --- a/test-data/b_gbk/snps.log Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,168 +0,0 @@ -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b_gbk --ref reference.gbk --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref - - -### bwa mem -Y -M -R '@RG\tID:b_gbk\tSM:b_gbk' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.22845. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.22845. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.22845. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b_gbk --ref reference.gbk --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref - - -### bwa mem -Y -M -R '@RG\tID:b_gbk\tSM:b_gbk' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.23270. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.23270. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.23270. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b_gbk --ref reference.gbk --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.004 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref - - -### bwa mem -Y -M -R '@RG\tID:b_gbk\tSM:b_gbk' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.23837. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.23837. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.23837. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf - diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/snps.raw.vcf --- a/test-data/b_gbk/snps.raw.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -##fileformat=VCFv4.2 -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b_gbk -reference 4 . A T 63.8794 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_gbk/snps.vcf diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/ref.fa Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,13 @@ +>reference +TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA +GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT +CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT +GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT +ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC +AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC +AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT +TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA +ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG +TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT +TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/ref.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/ref.fa.fai Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,1 @@ +reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/genomes/ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/reference/genomes/ref.fa Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,13 @@ +>reference +TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA +GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT +CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT +GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT +ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC +AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC +AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT +TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA +ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG +TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT +TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/reference/ref.fa Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,13 @@ +>reference +TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA +GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT +CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT +GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT +ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC +AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC +AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT +TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA +ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG +TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT +TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.fa.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/reference/ref.fa.amb Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,1 @@ +700 1 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.fa.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/reference/ref.fa.ann Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,3 @@ +700 1 11 +0 reference (null) +0 700 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.fa.bwt Binary file test-data/b_out_dev/reference/ref.fa.bwt has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/reference/ref.fa.fai Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,1 @@ +reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.fa.pac Binary file test-data/b_out_dev/reference/ref.fa.pac has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.fa.sa Binary file test-data/b_out_dev/reference/ref.fa.sa has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.gff diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/reference/ref.txt Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,1 @@ +reference:0-700 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/reference/ref/genes.gff.gz Binary file test-data/b_out_dev/reference/ref/genes.gff.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.aligned.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.aligned.fa Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,13 @@ +>reference +TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT--------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------- diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.bam Binary file test-data/b_out_dev/snps.bam has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.bam.bai Binary file test-data/b_out_dev/snps.bam.bai has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.bed Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,1 @@ +reference 3 4 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.consensus.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.consensus.fa Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,13 @@ +>reference +TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA +GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT +CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT +GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT +ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC +AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC +AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT +TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA +ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG +TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT +TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.consensus.subs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.consensus.subs.fa Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,13 @@ +>reference +TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA +GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT +CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT +GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT +ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC +AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC +AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT +TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA +ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG +TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT +TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.csv Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,2 @@ +CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,EFFECT,LOCUS_TAG,GENE,PRODUCT +reference,4,snp,A,T,T:10 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.filt.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.filt.vcf Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,28 @@ +##fileformat=VCFv4.2 +##FILTER= +##fileDate=20190312 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig= +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=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; Date=Tue Mar 12 14:35:28 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b +reference 4 . A T 321.326 . AB=0;AO=10;DP=10;QA=400;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:10:0:0:10:400:-36.3607,-3.0103,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.gff Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,2 @@ +##gff-version 3 +reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:10 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.html Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,24 @@ + + + +
CHROM +POS +TYPE +REF +ALT +EVIDENCE +FTYPE +STRAND +NT_POS +AA_POS +EFFECT +LOCUS_TAG +GENE +PRODUCT +
reference +4 +snp +A +T +T:10 A:0 +
diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.log Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,261 @@ +### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir b_out_dev --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq + +### samtools faidx reference/ref.fa + + +### bwa index reference/ref.fa + +[bwa_index] Pack FASTA... 0.00 sec +[bwa_index] Construct BWT for the packed sequence... +[bwa_index] 0.00 seconds elapse. +[bwa_index] Update BWT... 0.00 sec +[bwa_index] Pack forward-only FASTA... 0.00 sec +[bwa_index] Construct SA from BWT and Occ... 0.00 sec +[main] Version: 0.7.17-r1188 +[main] CMD: bwa index reference/ref.fa +[main] Real time: 0.009 sec; CPU: 0.003 sec + +### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa + + +### ln -sf reference/ref.fa . + + +### ln -sf reference/ref.fa.fai . + + +### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz + + +### bwa mem -Y -M -R '@RG\tID:b_out_dev\tSM:b_out_dev' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.9396. -r -s - - > snps.bam + +READ 10 WRITTEN 10 +EXCLUDED 0 EXAMINED 10 +PAIRED 10 SINGLE 0 +DULPICATE PAIR 0 DUPLICATE SINGLE 0 +DUPLICATE TOTAL 0 + +### samtools index snps.bam + + +### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt + + +### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf + + +### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' 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 + + +### cp snps.filt.vcf snps.vcf + + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab + +Loading reference: reference/ref.fa +Loaded 1 sequences. +Loading features: reference/ref.gff +Parsing variants: snps.vcf +Converted 1 SNPs to TAB format. + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf + + +### bcftools convert -Oz -o snps.vcf.gz snps.vcf + + +### bcftools index -f snps.vcf.gz + + +### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz + +Note: the --sample option not given, applying all records regardless of the genotype + +### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf + + +### bcftools index -f snps.subs.vcf.gz + + +### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz + +Note: the --sample option not given, applying all records regardless of the genotype + +### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi + +### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq + +### samtools faidx reference/ref.fa + + +### bwa index reference/ref.fa + +[bwa_index] Pack FASTA... 0.00 sec +[bwa_index] Construct BWT for the packed sequence... +[bwa_index] 0.00 seconds elapse. +[bwa_index] Update BWT... 0.00 sec +[bwa_index] Pack forward-only FASTA... 0.00 sec +[bwa_index] Construct SA from BWT and Occ... 0.00 sec +[main] Version: 0.7.17-r1188 +[main] CMD: bwa index reference/ref.fa +[main] Real time: 0.008 sec; CPU: 0.002 sec + +### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa + + +### ln -sf reference/ref.fa . + + +### ln -sf reference/ref.fa.fai . + + +### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz + + +### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.10001. -r -s - - > snps.bam + +READ 10 WRITTEN 10 +EXCLUDED 0 EXAMINED 10 +PAIRED 10 SINGLE 0 +DULPICATE PAIR 0 DUPLICATE SINGLE 0 +DUPLICATE TOTAL 0 + +### samtools index snps.bam + + +### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt + + +### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf + + +### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' 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 + + +### cp snps.filt.vcf snps.vcf + + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab + +Loading reference: reference/ref.fa +Loaded 1 sequences. +Loading features: reference/ref.gff +Parsing variants: snps.vcf +Converted 1 SNPs to TAB format. + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf + + +### bcftools convert -Oz -o snps.vcf.gz snps.vcf + + +### bcftools index -f snps.vcf.gz + + +### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz + +Note: the --sample option not given, applying all records regardless of the genotype + +### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf + + +### bcftools index -f snps.subs.vcf.gz + + +### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz + +Note: the --sample option not given, applying all records regardless of the genotype + +### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi + +### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq + +### samtools faidx reference/ref.fa + + +### bwa index reference/ref.fa + +[bwa_index] Pack FASTA... 0.00 sec +[bwa_index] Construct BWT for the packed sequence... +[bwa_index] 0.00 seconds elapse. +[bwa_index] Update BWT... 0.00 sec +[bwa_index] Pack forward-only FASTA... 0.00 sec +[bwa_index] Construct SA from BWT and Occ... 0.00 sec +[main] Version: 0.7.17-r1188 +[main] CMD: bwa index reference/ref.fa +[main] Real time: 0.009 sec; CPU: 0.003 sec + +### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa + + +### ln -sf reference/ref.fa . + + +### ln -sf reference/ref.fa.fai . + + +### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz + + +### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.22109. -r -s - - > snps.bam + +READ 10 WRITTEN 10 +EXCLUDED 0 EXAMINED 10 +PAIRED 10 SINGLE 0 +DULPICATE PAIR 0 DUPLICATE SINGLE 0 +DUPLICATE TOTAL 0 + +### samtools index snps.bam + + +### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt + + +### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf + + +### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' 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 + + +### cp snps.filt.vcf snps.vcf + + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab + +Loading reference: reference/ref.fa +Loaded 1 sequences. +Loading features: reference/ref.gff +Parsing variants: snps.vcf +Converted 1 SNPs to TAB format. + +### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf + + +### bcftools convert -Oz -o snps.vcf.gz snps.vcf + + +### bcftools index -f snps.vcf.gz + + +### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz + +Note: the --sample option not given, applying all records regardless of the genotype + +### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf + + +### bcftools index -f snps.subs.vcf.gz + + +### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz + +Note: the --sample option not given, applying all records regardless of the genotype + +### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi + diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.raw.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.raw.vcf Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,62 @@ +##fileformat=VCFv4.2 +##fileDate=20190312 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig= +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b +reference 4 . 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A T 321.326 . TYPE=snp;DP=10;RO=0;AO=10 GT:DP:RO:AO:QR:QA 1/1:10:0:10:0:400 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.tab Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,2 @@ +CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS EFFECT LOCUS_TAG GENE PRODUCT +reference 4 snp A T T:10 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.txt Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,7 @@ +DateTime 2019-03-12T14:35:28 +ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq +Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/ref.fna +ReferenceSize 700 +Software snippy 4.3.6 +Variant-SNP 1 +VariantTotal 1 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/b_out_dev/snps.vcf Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,28 @@ +##fileformat=VCFv4.2 +##FILTER= +##fileDate=20190312 +##source=freeBayes v1.2.0-dirty +##reference=reference/ref.fa +##contig= +##phasing=none +##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##bcftools_viewVersion=1.9+htslib-1.9 +##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 2019 +##bcftools_annotateVersion=1.9+htslib-1.9 +##bcftools_annotateCommand=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; Date=Tue Mar 12 14:35:28 2019 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b +reference 4 . A T 321.326 . AB=0;AO=10;DP=10;QA=400;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:10:0:0:10:400:-36.3607,-3.0103,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.vcf.gz Binary file test-data/b_out_dev/snps.vcf.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/b_out_dev/snps.vcf.gz.csi Binary file test-data/b_out_dev/snps.vcf.gz.csi has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/ref.fa --- a/test-data/c/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/ref.fa.fai --- a/test-data/c/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/genomes/ref.fa --- a/test-data/c/reference/genomes/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.fa --- a/test-data/c/reference/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.fa.amb --- a/test-data/c/reference/ref.fa.amb Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -700 1 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.fa.ann --- a/test-data/c/reference/ref.fa.ann Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -700 1 11 -0 reference (null) -0 700 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.fa.bwt Binary file test-data/c/reference/ref.fa.bwt has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.fa.fai --- a/test-data/c/reference/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.fa.pac Binary file test-data/c/reference/ref.fa.pac has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.fa.sa Binary file test-data/c/reference/ref.fa.sa has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.gff diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref.txt --- a/test-data/c/reference/ref.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference:0-700 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/reference/ref/genes.gff.gz Binary file test-data/c/reference/ref/genes.gff.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.aligned.fa --- a/test-data/c/snps.aligned.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTACACT--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------- diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.bam Binary file test-data/c/snps.bam has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.bam.bai Binary file test-data/c/snps.bam.bai has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.bed --- a/test-data/c/snps.bed Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 47 48 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.consensus.fa --- a/test-data/c/snps.consensus.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTACACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.consensus.subs.fa --- a/test-data/c/snps.consensus.subs.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTACACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.csv --- a/test-data/c/snps.csv Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,EFFECT,LOCUS_TAG,GENE,PRODUCT -reference,48,snp,A,C,C:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.filt.vcf --- a/test-data/c/snps.filt.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:42:19 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:42:19 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c -reference 48 . A C 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.gff --- a/test-data/c/snps.gff Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -##gff-version 3 -reference snippy:4.3.6 variation 48 48 . . 0 note=snp A=>C C:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.html --- a/test-data/c/snps.html Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ - - - -
CHROM -POS -TYPE -REF -ALT -EVIDENCE -FTYPE -STRAND -NT_POS -AA_POS -EFFECT -LOCUS_TAG -GENE -PRODUCT -
reference -48 -snp -A -C -C:2 A:0 -
diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.log --- a/test-data/c/snps.log Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,783 +0,0 @@ -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.13651. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.13651. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.13651. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### 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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.14000. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14000. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14000. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.14733. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14733. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14733. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 20 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.004 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.15004. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.15004. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.15004. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=20 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 1 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.17443. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.17443. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.17443. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 1 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.25837. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.25837. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.25837. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 80 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.26070. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.26070. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.26070. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=80 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 65 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.26290. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.26290. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.26290. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=65 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 0 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.070 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.26511. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.26511. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.26511. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 1 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.raw.vcf --- a/test-data/c/snps.raw.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -##fileformat=VCFv4.2 -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c -reference 48 . A C 63.8794 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=2;RPP=7.35324;RPPR=0;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.subs.vcf --- a/test-data/c/snps.subs.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -##fileformat=VCFv4.2 -##snippy="snippy-vcf_extract_subs snps.filt.vcf" -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:42:19 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:42:19 2019 -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c -reference 48 . A C 63.8794 . TYPE=snp;DP=2;RO=0;AO=2 GT:DP:RO:AO:QR:QA 1/1:2:0:2:0:80 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.tab --- a/test-data/c/snps.tab Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS EFFECT LOCUS_TAG GENE PRODUCT -reference 48 snp A C C:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.txt --- a/test-data/c/snps.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -DateTime 2019-02-06T12:42:18 -ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq -Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/reference.fasta -ReferenceSize 700 -Software snippy 4.3.6 -Variant-SNP 1 -VariantTotal 1 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.vcf --- a/test-data/c/snps.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:42:19 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:42:19 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c -reference 48 . A C 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.vcf.gz Binary file test-data/c/snps.vcf.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c/snps.vcf.gz.csi Binary file test-data/c/snps.vcf.gz.csi has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/ref.fa --- a/test-data/c_gbk/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/ref.fa.fai --- a/test-data/c_gbk/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 49 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/genomes/ref.fa --- a/test-data/c_gbk/reference/genomes/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference Listeria monocytogenes strain strain. -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.fa --- a/test-data/c_gbk/reference/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.fa.amb --- a/test-data/c_gbk/reference/ref.fa.amb Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -700 1 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.fa.ann --- a/test-data/c_gbk/reference/ref.fa.ann Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -700 1 11 -0 reference Listeria monocytogenes strain strain. -0 700 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.fa.bwt Binary file test-data/c_gbk/reference/ref.fa.bwt has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.fa.fai --- a/test-data/c_gbk/reference/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 49 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.fa.pac Binary file test-data/c_gbk/reference/ref.fa.pac has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.fa.sa Binary file test-data/c_gbk/reference/ref.fa.sa has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.gff --- a/test-data/c_gbk/reference/ref.gff Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -##gff-version 3 -reference snippy CDS 188 658 . + 0 ID=KPFNHDNB_00001;codon_start=1;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPFNHDNB_00001;product=hypothetical protein;transl_table=11;translation=MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref.txt --- a/test-data/c_gbk/reference/ref.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference:0-700 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref/genes.gff.gz Binary file test-data/c_gbk/reference/ref/genes.gff.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/ref/snpEffectPredictor.bin Binary file test-data/c_gbk/reference/ref/snpEffectPredictor.bin has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/reference/snpeff.config --- a/test-data/c_gbk/reference/snpeff.config Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -codon.Standard : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Vertebrate_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/*, AGG/*, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Yeast_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/T, CTC/T, CTA/T, CTG/T, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Mold_Mitochondrial : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Protozoan_Mitochondrial : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Coelenterate : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Mitochondrial : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Mycoplasma : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Spiroplasma : TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Invertebrate_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Ciliate_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Dasycladacean_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Hexamita_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Echinoderm_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Flatworm_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Euplotid_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/C, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Bacterial_and_Plant_Plastid : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Alternative_Yeast_Nuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Ascidian_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Alternative_Flatworm_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Blepharisma_Macronuclear : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Chlorophycean_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Trematode_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Scenedesmus_obliquus_Mitochondrial : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -codon.Thraustochytrium_Mitochondrial : TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G -ref.genome : Snippy Reference - ref.chromosome : reference - ref.reference.codonTable : Bacterial_and_Plant_Plastid diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/snps.bam Binary file test-data/c_gbk/snps.bam has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/snps.bam.bai Binary file test-data/c_gbk/snps.bam.bai has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/snps.filt.vcf --- a/test-data/c_gbk/snps.filt.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb 6 12:30:20 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Wed Feb 6 12:30:20 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c_gbk -reference 48 . A C 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/snps.log --- a/test-data/c_gbk/snps.log Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir c_gbk --ref reference.gbk --R1 c_1.fastq --R2 c_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.071 sec; CPU: 0.004 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref - - -### bwa mem -Y -M -R '@RG\tID:c_gbk\tSM:c_gbk' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.24822. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.24822. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.24822. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (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 - - -### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf - diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/snps.raw.vcf --- a/test-data/c_gbk/snps.raw.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -##fileformat=VCFv4.2 -##fileDate=20190206 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c_gbk -reference 48 . A C 63.8794 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=2;RPP=7.35324;RPPR=0;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/c_gbk/snps.vcf diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/ref.fa --- a/test-data/fna_ref_b_testing/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/ref.fa.fai --- a/test-data/fna_ref_b_testing/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/genomes/ref.fa --- a/test-data/fna_ref_b_testing/reference/genomes/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.fa --- a/test-data/fna_ref_b_testing/reference/ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.fa.amb --- a/test-data/fna_ref_b_testing/reference/ref.fa.amb Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -700 1 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.fa.ann --- a/test-data/fna_ref_b_testing/reference/ref.fa.ann Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -700 1 11 -0 reference (null) -0 700 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.fa.bwt Binary file test-data/fna_ref_b_testing/reference/ref.fa.bwt has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.fa.fai --- a/test-data/fna_ref_b_testing/reference/ref.fa.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 60 61 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.fa.pac Binary file test-data/fna_ref_b_testing/reference/ref.fa.pac has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.fa.sa Binary file test-data/fna_ref_b_testing/reference/ref.fa.sa has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.gff diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref.txt --- a/test-data/fna_ref_b_testing/reference/ref.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference:0-700 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/reference/ref/genes.gff.gz Binary file test-data/fna_ref_b_testing/reference/ref/genes.gff.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.aligned.fa --- a/test-data/fna_ref_b_testing/snps.aligned.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------- diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.bam Binary file test-data/fna_ref_b_testing/snps.bam has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.bam.bai Binary file test-data/fna_ref_b_testing/snps.bam.bai has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.bed --- a/test-data/fna_ref_b_testing/snps.bed Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 3 4 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.consensus.fa --- a/test-data/fna_ref_b_testing/snps.consensus.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.consensus.subs.fa --- a/test-data/fna_ref_b_testing/snps.consensus.subs.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.csv --- a/test-data/fna_ref_b_testing/snps.csv Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,EFFECT,LOCUS_TAG,GENE,PRODUCT -reference,4,snp,A,T,T:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.filt.vcf --- a/test-data/fna_ref_b_testing/snps.filt.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190211 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Mon Feb 11 11:46:35 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Mon Feb 11 11:46:35 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fna_ref_b_testing -reference 4 . A T 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.gff --- a/test-data/fna_ref_b_testing/snps.gff Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -##gff-version 3 -reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.html --- a/test-data/fna_ref_b_testing/snps.html Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ - - - -
CHROM -POS -TYPE -REF -ALT -EVIDENCE -FTYPE -STRAND -NT_POS -AA_POS -EFFECT -LOCUS_TAG -GENE -PRODUCT -
reference -4 -snp -A -T -T:2 A:0 -
diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.log --- a/test-data/fna_ref_b_testing/snps.log Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir fna_ref_b_testing --cpus 1 --ref reference.fasta --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq - -### samtools faidx reference/ref.fa - - -### bwa index reference/ref.fa - -[bwa_index] Pack FASTA... 0.00 sec -[bwa_index] Construct BWT for the packed sequence... -[bwa_index] 0.00 seconds elapse. -[bwa_index] Update BWT... 0.00 sec -[bwa_index] Pack forward-only FASTA... 0.00 sec -[bwa_index] Construct SA from BWT and Occ... 0.00 sec -[main] Version: 0.7.17-r1188 -[main] CMD: bwa index reference/ref.fa -[main] Real time: 0.009 sec; CPU: 0.003 sec - -### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa - - -### ln -sf reference/ref.fa . - - -### ln -sf reference/ref.fa.fai . - - -### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz - - -### bwa mem -Y -M -R '@RG\tID:fna_ref_b_testing\tSM:fna_ref_b_testing' -t 1 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.8702. --threads 1 -m 8000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.8702. --threads 1 -m 8000M | samtools markdup -T /tmp/snippy.8702. -r -s - - > snps.bam - -READ 10 WRITTEN 2 -EXCLUDED 0 EXAMINED 10 -PAIRED 10 SINGLE 0 -DULPICATE PAIR 8 DUPLICATE SINGLE 0 -DUPLICATE TOTAL 8 - -### samtools index snps.bam - - -### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt - - -### freebayes-parallel reference/ref.txt 1 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf - - -### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' 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 - - -### cp snps.filt.vcf snps.vcf - - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab - -Loading reference: reference/ref.fa -Loaded 1 sequences. -Loading features: reference/ref.gff -Parsing variants: snps.vcf -Converted 1 SNPs to TAB format. - -### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf - - -### bcftools convert -Oz -o snps.vcf.gz snps.vcf - - -### bcftools index -f snps.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf - - -### bcftools index -f snps.subs.vcf.gz - - -### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz - -Note: the --sample option not given, applying all records regardless of the genotype - -### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi - diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.raw.vcf --- a/test-data/fna_ref_b_testing/snps.raw.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -##fileformat=VCFv4.2 -##fileDate=20190211 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fna_ref_b_testing -reference 4 . A T 63.8794 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.subs.vcf --- a/test-data/fna_ref_b_testing/snps.subs.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -##fileformat=VCFv4.2 -##snippy="snippy-vcf_extract_subs snps.filt.vcf" -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190211 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Mon Feb 11 11:46:35 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Mon Feb 11 11:46:35 2019 -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fna_ref_b_testing -reference 4 . A T 63.8794 . TYPE=snp;DP=2;RO=0;AO=2 GT:DP:RO:AO:QR:QA 1/1:2:0:2:0:80 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.tab --- a/test-data/fna_ref_b_testing/snps.tab Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS EFFECT LOCUS_TAG GENE PRODUCT -reference 4 snp A T T:2 A:0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.txt --- a/test-data/fna_ref_b_testing/snps.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -DateTime 2019-02-11T11:46:34 -ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq -Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/reference.fasta -ReferenceSize 700 -Software snippy 4.3.6 -Variant-SNP 1 -VariantTotal 1 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.vcf --- a/test-data/fna_ref_b_testing/snps.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190211 -##source=freeBayes v1.2.0-dirty -##reference=reference/ref.fa -##contig= -##phasing=none -##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700" -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##bcftools_viewVersion=1.9+htslib-1.9 -##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Mon Feb 11 11:46:35 2019 -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=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; Date=Mon Feb 11 11:46:35 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT fna_ref_b_testing -reference 4 . A T 63.8794 . AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:80:-7.59179,-0.60206,0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.vcf.gz Binary file test-data/fna_ref_b_testing/snps.vcf.gz has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/fna_ref_b_testing/snps.vcf.gz.csi Binary file test-data/fna_ref_b_testing/snps.vcf.gz.csi has changed diff -r 3bbfe41787af -r 0e733df972b5 test-data/gbk_ref_b/snps.vcf diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.err --- a/test-data/prokka-out/PROKKA_02062019.err Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -Discrepancy Report Results - -Summary -DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein" -FATAL: MISSING_PROTEIN_ID:1 proteins have invalid IDs. -DISC_SOURCE_QUALS_ASNDISC:strain (all present, all unique) -DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all unique) -DISC_FEATURE_COUNT:CDS: 1 present -DISC_COUNT_NUCLEOTIDES:1 nucleotide Bioseqs are present -FEATURE_LOCATION_CONFLICT:1 features have inconsistent gene locations. -DISC_QUALITY_SCORES:Quality scores are missing on all sequences. -ONCALLER_COMMENT_PRESENT:1 comment descriptors were found (all same) -MISSING_GENOMEASSEMBLY_COMMENTS:1 bioseqs are missing GenomeAssembly structured comments -MOLTYPE_NOT_MRNA:1 molecule types are not set as mRNA. -TECHNIQUE_NOT_TSA:1 technique are not set as TSA -MISSING_STRUCTURED_COMMENT:1 sequences do not include structured comments. -MISSING_PROJECT:2 sequences do not include project. -DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same) - - -Detailed Report - -DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein" - -FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::1 proteins have invalid IDs. -prokka-out/PROKKA_02062019:reference_1 (length 156) - -DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all unique) -DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for strain -DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all unique) -DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for taxname -DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 1 present -DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::1 nucleotide Bioseqs are present -prokka-out/PROKKA_02062019:reference (length 700) - -DiscRep_ALL:FEATURE_LOCATION_CONFLICT::1 features have inconsistent gene locations. -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -prokka-out/PROKKA_02062019:CDS hypothetical protein reference:188-658 KPFNHDNB_00001 - -DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences. - -DiscRep_ALL:ONCALLER_COMMENT_PRESENT::1 comment descriptors were found (all same) -prokka-out/PROKKA_02062019:reference:Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka - -DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::1 bioseqs are missing GenomeAssembly structured comments -prokka-out/PROKKA_02062019:reference (length 700) - -DiscRep_ALL:MOLTYPE_NOT_MRNA::1 molecule types are not set as mRNA. -prokka-out/PROKKA_02062019:reference (length 700) - -DiscRep_ALL:TECHNIQUE_NOT_TSA::1 technique are not set as TSA -prokka-out/PROKKA_02062019:reference (length 700) - -DiscRep_ALL:MISSING_STRUCTURED_COMMENT::1 sequences do not include structured comments. -prokka-out/PROKKA_02062019:reference (length 700) - -DiscRep_ALL:MISSING_PROJECT::2 sequences do not include project. -prokka-out/PROKKA_02062019:reference (length 700) -prokka-out/PROKKA_02062019:reference_1 (length 156) - -DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same) -DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing) -DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::1 Molinfos are missing field technique -prokka-out/PROKKA_02062019:reference (length 700) - diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.faa --- a/test-data/prokka-out/PROKKA_02062019.faa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->KPFNHDNB_00001 hypothetical protein -MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKEAFSVN -IKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYP -AEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.ffn --- a/test-data/prokka-out/PROKKA_02062019.ffn Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ ->KPFNHDNB_00001 hypothetical protein -ATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTATACAAAAC -AGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACCAGCAGAA -ATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTCAGTGAAT -ATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGAAGAACAG -GAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCA -GAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCT -GCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAA -ATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAA diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.fna --- a/test-data/prokka-out/PROKKA_02062019.fna Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.fsa --- a/test-data/prokka-out/PROKKA_02062019.fsa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ ->reference [gcode=11] [organism=Listeria monocytogenes] [strain=strain] -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.gbk --- a/test-data/prokka-out/PROKKA_02062019.gbk Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -LOCUS reference 700 bp DNA linear 06-FEB-2019 -DEFINITION Listeria monocytogenes strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Listeria monocytogenes - ORGANISM Listeria monocytogenes - Unclassified. -COMMENT Annotated using prokka 1.13.3 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..700 - /organism="Listeria monocytogenes" - /mol_type="genomic DNA" - /strain="strain" - CDS 188..658 - /locus_tag="KPFNHDNB_00001" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDF - KVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPET - SHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ" -ORIGIN - 1 tccacaagcc attgtgtgta attaaccact aattgtgtat aagtttaaac taattgaaaa - 61 ggttatccac aataaaaagg cgttattcag gagttatcca cactttctag gaaaggattt - 121 cattgcgcca atgtgttaaa ctatttaccg aatacgaaaa aaagacaaat aaatgaggtt - 181 gtgaaaaatg atatttcaac ggcttttgaa aactagagat acagagtttt atcgagttat - 241 acaaaacagg aatattgacg acgtatttgg atacttatta attcacgata aacgggaacc - 301 agcagaaatt gacgatttta aggtatttgc aaaaagtaat ataaataaag aagctttttc - 361 agtgaatatc aaaaaaaatc atatttacac gatgtttttc cactttactg atttagagga - 421 agaacaggaa attccaaaat ttactaaagt tattcgtttt atagaaggac ttttatcttt - 481 tcagccagaa acaagccatt acgttgataa ctatttaata aaggaaaaac taatttttga - 541 atatcctgct gaatttgaga aaatcgggga gtttgctaaa tatttagtaa agctttcggg - 601 tcgtaaaatt actattccag acacaacgag agaaaaatat atctatttaa cgcaataatt - 661 ttcgaaaaat ggtttttctc tctataaaaa tatgatatga -// diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.gff --- a/test-data/prokka-out/PROKKA_02062019.gff Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -##gff-version 3 -##sequence-region reference 1 700 -reference Prodigal:2.6 CDS 188 658 . + 0 ID=KPFNHDNB_00001;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPFNHDNB_00001;product=hypothetical protein -##FASTA ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.log --- a/test-data/prokka-out/PROKKA_02062019.log Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -[11:29:26] This is prokka 1.13.3 -[11:29:26] Written by Torsten Seemann -[11:29:26] Homepage is https://github.com/tseemann/prokka -[11:29:26] Local time is Wed Feb 6 11:29:26 2019 -[11:29:26] You are dfornika -[11:29:26] Operating system is linux -[11:29:26] You have BioPerl 1.007002 -[11:29:26] System has 8 cores. -[11:29:26] Will use maximum of 8 cores. -[11:29:26] Annotating as >>> Bacteria <<< -[11:29:26] Generating locus_tag from 'reference.fasta' contents. -[11:29:26] Setting --locustag KPFNHDNB from MD5 49f71d7b5d5a34956f52c337db5c3269 -[11:29:26] Re-using existing --outdir prokka-out -[11:29:26] Using filename prefix: PROKKA_02062019.XXX -[11:29:26] Setting HMMER_NCPU=1 -[11:29:26] Writing log to: prokka-out/PROKKA_02062019.log -[11:29:26] Command: /home/dfornika/miniconda3/envs/prokka-1.13/bin/prokka reference.fasta --genus Listeria --species monocytogenes --outdir prokka-out --force -[11:29:26] Appending to PATH: /home/dfornika/miniconda3/envs/prokka-1.13/bin -[11:29:26] Looking for 'aragorn' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/aragorn -[11:29:26] Determined aragorn version is 1.2 -[11:29:26] Looking for 'barrnap' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/barrnap -[11:29:26] Determined barrnap version is 0.9 -[11:29:26] Looking for 'blastp' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/blastp -[11:29:26] Determined blastp version is 2.7 -[11:29:26] Looking for 'cmpress' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/cmpress -[11:29:26] Determined cmpress version is 1.1 -[11:29:26] Looking for 'cmscan' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/cmscan -[11:29:26] Determined cmscan version is 1.1 -[11:29:26] Looking for 'egrep' - found /usr/bin/egrep -[11:29:26] Looking for 'find' - found /usr/bin/find -[11:29:26] Looking for 'grep' - found /usr/bin/grep -[11:29:26] Looking for 'hmmpress' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/hmmpress -[11:29:26] Determined hmmpress version is 3.2 -[11:29:26] Looking for 'hmmscan' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/hmmscan -[11:29:26] Determined hmmscan version is 3.2 -[11:29:26] Looking for 'java' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/java -[11:29:26] Looking for 'less' - found /usr/bin/less -[11:29:26] Looking for 'makeblastdb' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/makeblastdb -[11:29:26] Determined makeblastdb version is 2.7 -[11:29:26] Looking for 'minced' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/minced -[11:29:26] Determined minced version is 3.2 -[11:29:26] Looking for 'parallel' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/parallel -[11:29:26] Determined parallel version is 20181022 -[11:29:26] Looking for 'prodigal' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/prodigal -[11:29:26] Determined prodigal version is 2.6 -[11:29:26] Looking for 'prokka-genbank_to_fasta_db' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/prokka-genbank_to_fasta_db -[11:29:26] Looking for 'sed' - found /usr/bin/sed -[11:29:26] Looking for 'tbl2asn' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/tbl2asn -[11:29:26] Determined tbl2asn version is 25.6 -[11:29:26] Using genetic code table 11. -[11:29:26] Loading and checking input file: reference.fasta -[11:29:26] Wrote 1 contigs totalling 700 bp. -[11:29:26] Predicting tRNAs and tmRNAs -[11:29:26] Running: aragorn -l -gc11 -w prokka\-out\/PROKKA_02062019\.fna -[11:29:26] Found 0 tRNAs -[11:29:26] Predicting Ribosomal RNAs -[11:29:26] Running Barrnap with 8 threads -[11:29:26] Found 0 rRNAs -[11:29:26] Skipping ncRNA search, enable with --rfam if desired. -[11:29:26] Total of 0 tRNA + rRNA features -[11:29:26] Searching for CRISPR repeats -[11:29:26] Found 0 CRISPRs -[11:29:26] Predicting coding sequences -[11:29:26] Contigs total 700 bp, so using meta mode -[11:29:26] Running: prodigal -i prokka\-out\/PROKKA_02062019\.fna -c -m -g 11 -p meta -f sco -q -[11:29:26] Found 1 CDS -[11:29:26] Connecting features back to sequences -[11:29:26] Not using genus-specific database. Try --usegenus to enable it. -[11:29:26] Annotating CDS, please be patient. -[11:29:26] Will use 8 CPUs for similarity searching. -[11:29:26] There are still 1 unannotated CDS left (started with 1) -[11:29:26] Will use blast to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/IS with 8 CPUs -[11:29:26] Running: cat prokka\-out\/IS\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe blastp -query - -db /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\-out\/IS\.blast 2> /dev/null -[11:29:27] Deleting unwanted file: prokka-out/IS.faa -[11:29:27] Deleting unwanted file: prokka-out/IS.blast -[11:29:27] There are still 1 unannotated CDS left (started with 1) -[11:29:27] Will use blast to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/AMR with 8 CPUs -[11:29:27] Running: cat prokka\-out\/AMR\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe blastp -query - -db /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\-out\/AMR\.blast 2> /dev/null -[11:29:27] Deleting unwanted file: prokka-out/AMR.faa -[11:29:27] Deleting unwanted file: prokka-out/AMR.blast -[11:29:27] There are still 1 unannotated CDS left (started with 1) -[11:29:27] Will use blast to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/sprot with 8 CPUs -[11:29:27] Running: cat prokka\-out\/sprot\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe blastp -query - -db /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\-out\/sprot\.blast 2> /dev/null -[11:29:27] Deleting unwanted file: prokka-out/sprot.faa -[11:29:27] Deleting unwanted file: prokka-out/sprot.blast -[11:29:27] There are still 1 unannotated CDS left (started with 1) -[11:29:27] Will use hmmer3 to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/hmm/HAMAP.hmm with 8 CPUs -[11:29:27] Running: cat prokka\-out\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /home/dfornika/miniconda3/envs/prokka-1.13/db/hmm/HAMAP.hmm /dev/stdin > prokka\-out\/HAMAP\.hmm\.hmmer3 2> /dev/null -[11:29:28] Deleting unwanted file: prokka-out/HAMAP.hmm.faa -[11:29:28] Deleting unwanted file: prokka-out/HAMAP.hmm.hmmer3 -[11:29:28] Labelling remaining 1 proteins as 'hypothetical protein' -[11:29:28] Found 0 unique /gene codes. -[11:29:28] Fixed 0 colliding /gene names. -[11:29:28] Adding /locus_tag identifiers -[11:29:28] Assigned 1 locus_tags to CDS and RNA features. -[11:29:28] Writing outputs to prokka-out/ -[11:29:28] Generating annotation statistics file -[11:29:28] Generating Genbank and Sequin files -[11:29:28] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka' -Z prokka\-out\/PROKKA_02062019\.err -i prokka\-out\/PROKKA_02062019\.fsa 2> /dev/null -[11:29:28] Deleting unwanted file: prokka-out/errorsummary.val -[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.dr -[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.fixedproducts -[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.ecn -[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.val -[11:29:28] Repairing broken .GBK output that tbl2asn produces... -[11:29:28] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < prokka\-out\/PROKKA_02062019\.gbf > prokka\-out\/PROKKA_02062019\.gbk -[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.gbf -[11:29:28] Output files: -[11:29:28] prokka-out/PROKKA_02062019.faa -[11:29:28] prokka-out/PROKKA_02062019.log -[11:29:28] prokka-out/PROKKA_02062019.tbl -[11:29:28] prokka-out/PROKKA_02062019.ffn -[11:29:28] prokka-out/PROKKA_02062019.err -[11:29:28] prokka-out/PROKKA_02062019.txt -[11:29:28] prokka-out/PROKKA_02062019.gff -[11:29:28] prokka-out/PROKKA_02062019.tsv -[11:29:28] prokka-out/PROKKA_02062019.sqn -[11:29:28] prokka-out/PROKKA_02062019.fna -[11:29:28] prokka-out/PROKKA_02062019.fsa -[11:29:28] prokka-out/PROKKA_02062019.gbk -[11:29:28] Annotation finished successfully. -[11:29:28] Walltime used: 0.03 minutes -[11:29:28] If you use this result please cite the Prokka paper: -[11:29:28] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[11:29:28] Type 'prokka --citation' for more details. -[11:29:28] Thank you, come again. diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.sqn --- a/test-data/prokka-out/PROKKA_02062019.sqn Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -Seq-entry ::= set { - class genbank , - seq-set { - set { - class nuc-prot , - descr { - source { - org { - taxname "Listeria monocytogenes" , - orgname { - mod { - { - subtype strain , - subname "strain" } } , - gcode 11 } } } , - comment "Annotated using prokka 1.13.3 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 2 } , - { - label - str "day" , - data - int 6 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 6 } } , - seq-set { - seq { - id { - local - str "reference" } , - descr { - molinfo { - biomol genomic } } , - inst { - repr raw , - mol dna , - length 700 , - seq-data - iupacna "TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATT -GAAAAGGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATG -TGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAAA -ACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGAT -AAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTCAGTGAAT -ATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGAAGAACAGGAAATTCCAAAATTTACT -AAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAG -GAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGT -CGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCT -CTCTATAAAAATATGATATGA" } } , - seq { - id { - local - str "reference_1" } , - descr { - title "hypothetical protein KPFNHDNB_00001 [Listeria - monocytogenes]" , - molinfo { - biomol peptide , - tech concept-trans } } , - inst { - repr raw , - mol aa , - length 156 , - seq-data - ncbieaa "MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKE -AFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYPAEFEKIGEFAKYL -VKLSGRKITIPDTTREKYIYLTQ" } , - annot { - { - data - ftable { - { - id - local - id 2 , - data - prot { - name { - "hypothetical protein" } } , - location - int { - from 0 , - to 155 , - id - local - str "reference_1" } } } } } } } , - annot { - { - data - ftable { - { - id - local - id 1 , - data - cdregion { - frame one , - code { - id 11 } } , - product - whole - local - str "reference_1" , - location - int { - from 187 , - to 657 , - strand plus , - id - local - str "reference" } , - qual { - { - qual "inference" , - val "ab initio prediction:Prodigal:2.6" } } , - xref { - { - data - gene { - locus-tag "KPFNHDNB_00001" } } } } } } } } } } diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.tbl --- a/test-data/prokka-out/PROKKA_02062019.tbl Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ ->Feature reference -188 658 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag KPFNHDNB_00001 - product hypothetical protein diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.tsv --- a/test-data/prokka-out/PROKKA_02062019.tsv Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -locus_tag ftype length_bp gene EC_number COG product -KPFNHDNB_00001 CDS 471 hypothetical protein diff -r 3bbfe41787af -r 0e733df972b5 test-data/prokka-out/PROKKA_02062019.txt --- a/test-data/prokka-out/PROKKA_02062019.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -organism: Listeria monocytogenes strain -contigs: 1 -bases: 700 -CDS: 1 diff -r 3bbfe41787af -r 0e733df972b5 test-data/ref.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fna Tue Mar 12 17:37:29 2019 -0400 @@ -0,0 +1,11 @@ +>reference +TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAAGGTTATCCAC +AATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATGTGTTAAA +CTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAA +AACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTA +ATTCACGATAAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAG +AAGCTTTTTCAGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA +AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAA +ACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGA +AAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAAATTACTATTCCAGACACAACGAG +AGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/reference.fasta.fai --- a/test-data/reference.fasta.fai Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -reference 700 11 70 71 diff -r 3bbfe41787af -r 0e733df972b5 test-data/reference.gbk --- a/test-data/reference.gbk Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -LOCUS reference 700 bp DNA linear 06-FEB-2019 -DEFINITION Listeria monocytogenes strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Listeria monocytogenes - ORGANISM Listeria monocytogenes - Unclassified. -COMMENT Annotated using prokka 1.13.3 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..700 - /organism="Listeria monocytogenes" - /mol_type="genomic DNA" - /strain="strain" - CDS 188..658 - /locus_tag="KPFNHDNB_00001" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDF - KVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPET - SHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ" -ORIGIN - 1 tccacaagcc attgtgtgta attaaccact aattgtgtat aagtttaaac taattgaaaa - 61 ggttatccac aataaaaagg cgttattcag gagttatcca cactttctag gaaaggattt - 121 cattgcgcca atgtgttaaa ctatttaccg aatacgaaaa aaagacaaat aaatgaggtt - 181 gtgaaaaatg atatttcaac ggcttttgaa aactagagat acagagtttt atcgagttat - 241 acaaaacagg aatattgacg acgtatttgg atacttatta attcacgata aacgggaacc - 301 agcagaaatt gacgatttta aggtatttgc aaaaagtaat ataaataaag aagctttttc - 361 agtgaatatc aaaaaaaatc atatttacac gatgtttttc cactttactg atttagagga - 421 agaacaggaa attccaaaat ttactaaagt tattcgtttt atagaaggac ttttatcttt - 481 tcagccagaa acaagccatt acgttgataa ctatttaata aaggaaaaac taatttttga - 541 atatcctgct gaatttgaga aaatcgggga gtttgctaaa tatttagtaa agctttcggg - 601 tcgtaaaatt actattccag acacaacgag agaaaaatat atctatttaa cgcaataatt - 661 ttcgaaaaat ggtttttctc tctataaaaa tatgatatga -// diff -r 3bbfe41787af -r 0e733df972b5 test-data/snippy-core-out/core.aln --- a/test-data/snippy-core-out/core.aln Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ ->Reference -AA ->a -AA ->b -TA ->c -AC diff -r 3bbfe41787af -r 0e733df972b5 test-data/snippy-core-out/core.full.aln --- a/test-data/snippy-core-out/core.full.aln Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ ->Reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA -GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT -CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT -GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT -ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC -AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC -AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT -TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA -ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG -TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT -TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA ->a -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------- ->b -TCCtCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------- ->c -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAcACT--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------- diff -r 3bbfe41787af -r 0e733df972b5 test-data/snippy-core-out/core.ref.fa --- a/test-data/snippy-core-out/core.ref.fa Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ ->reference -TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAAGGTTATCCAC -AATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATGTGTTAAA -CTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAA -AACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTA -ATTCACGATAAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAG -AAGCTTTTTCAGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA -AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAA -ACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGA -AAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAAATTACTATTCCAGACACAACGAG -AGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA diff -r 3bbfe41787af -r 0e733df972b5 test-data/snippy-core-out/core.tab --- a/test-data/snippy-core-out/core.tab Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -CHR POS REF a b c -reference 4 A A T A -reference 48 A A A C diff -r 3bbfe41787af -r 0e733df972b5 test-data/snippy-core-out/core.txt --- a/test-data/snippy-core-out/core.txt Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -ID LENGTH ALIGNED UNALIGNED VARIANT HET MASKED LOWCOV -a 700 51 649 0 0 0 0 -b 700 51 649 1 0 0 0 -c 700 51 649 1 0 0 0 -Reference 700 700 0 0 0 0 0 diff -r 3bbfe41787af -r 0e733df972b5 test-data/snippy-core-out/core.vcf --- a/test-data/snippy-core-out/core.vcf Fri Mar 08 20:46:56 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -##fileformat=VCFv4.2 -##commandLine="snippy-core --ref reference.fasta a b c" -##FORMAT= -##INFO= -##contig= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT a b c -reference 4 . A T . PASS TYPE=snp GT 0 1 0 -reference 48 . A C . PASS TYPE=snp GT 0 0 1