snippy: test-data/c/snps.log annotate

annotate test-data/c/snps.log @ 20:3bbfe41787af draft

planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty

author	dfornika
date	Fri, 08 Mar 2019 20:46:56 -0500
parents
children

rev	line source
20 3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	1 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	3 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_2.fastq
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	4
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	5 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	6
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	7
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	8 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	9
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	10 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	11 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	12 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	13 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	14 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	15 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	16 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	17 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	18 [main] Real time: 0.070 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	19
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	20 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	21
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	22
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	23 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	24
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	25
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	26 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	27
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	28
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	29 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	30
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	31
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	32 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	33
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	34 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	35 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	36 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	37 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	38 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	39
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	40 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	41
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	42
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	43 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	44
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	45
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	46 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	47
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	48
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	49 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	50
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	51
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	52 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	53
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	54
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	55 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	56
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	57 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	58 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	59 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	60 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	61 Converted 0 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	62
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	63 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	64
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	65
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	66 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	67
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	68
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	69 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	70
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	71
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	72 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	73
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	74 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	75
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	76 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	77
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	78
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	79 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	80
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	81
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	82 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	83
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	84 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	85
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	86 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	87
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	88 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	89
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	90 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	91
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	92 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	93
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	94
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	95 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	96
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	97 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	98 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	99 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	100 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	101 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	102 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	103 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	104 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	105 [main] Real time: 0.070 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	106
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	107 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	108
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	109
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	110 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	111
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	112
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	113 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	114
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	115
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	116 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	117
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	118
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	119 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	120
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	121 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	122 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	123 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	124 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	125 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	126
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	127 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	128
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	129
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	130 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	131
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	132
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	133 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	134
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	135
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	136 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	137
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	138
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	139 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	140
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	141
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	142 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	143
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	144 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	145 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	146 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	147 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	148 Converted 0 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	149
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	150 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	151
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	152
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	153 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	154
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	155
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	156 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	157
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	158
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	159 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	160
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	161 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	162
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	163 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	164
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	165
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	166 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	167
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	168
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	169 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	170
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	171 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	172
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	173 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	174
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	175 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	176
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	177 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	178
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	179 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	180
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	181
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	182 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	183
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	184 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	185 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	186 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	187 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	188 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	189 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	190 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	191 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	192 [main] Real time: 0.070 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	193
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	194 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	195
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	196
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	197 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	198
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	199
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	200 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	201
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	202
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	203 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	204
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	205
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	206 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	207
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	208 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	209 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	210 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	211 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	212 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	213
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	214 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	215
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	216
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	217 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	218
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	219
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	220 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	221
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	222
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	223 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	224
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	225
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	226 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	227
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	228
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	229 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	230
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	231 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	232 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	233 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	234 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	235 Converted 0 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	236
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	237 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	238
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	239
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	240 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	241
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	242
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	243 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	244
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	245
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	246 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	247
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	248 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	249
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	250 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	251
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	252
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	253 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	254
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	255
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	256 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	257
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	258 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	259
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	260 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	261
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	262 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	263
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	264 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	265
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	266 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	267
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	268
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	269 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	270
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	271 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	272 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	273 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	274 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	275 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	276 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	277 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	278 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	279 [main] Real time: 0.070 sec; CPU: 0.004 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	280
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	281 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	282
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	283
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	284 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	285
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	286
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	287 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	288
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	289
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	290 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	291
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	292
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	293 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	294
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	295 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	296 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	297 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	298 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	299 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	300
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	301 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	302
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	303
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	304 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	305
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	306
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	307 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	308
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	309
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	310 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	311
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	312
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	313 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	314
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	315
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	316 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	317
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	318 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	319 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	320 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	321 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	322 Converted 1 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	323
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	324 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	325
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	326
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	327 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	328
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	329
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	330 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	331
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	332
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	333 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	334
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	335 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	336
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	337 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	338
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	339
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	340 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	341
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	342
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	343 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	344
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	345 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	346
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	347 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	348
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	349 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	350
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	351 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	352
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	353 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	354
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	355
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	356 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	357
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	358 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	359 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	360 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	361 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	362 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	363 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	364 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	365 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	366 [main] Real time: 0.071 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	367
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	368 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	369
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	370
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	371 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	372
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	373
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	374 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	375
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	376
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	377 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	378
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	379
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	380 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	381
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	382 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	383 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	384 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	385 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	386 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	387
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	388 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	389
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	390
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	391 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	392
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	393
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	394 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	395
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	396
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	397 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	398
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	399
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	400 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	401
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	402
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	403 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	404
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	405 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	406 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	407 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	408 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	409 Converted 1 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	410
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	411 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	412
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	413
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	414 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	415
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	416
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	417 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	418
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	419
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	420 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	421
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	422 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	423
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	424 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	425
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	426
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	427 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	428
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	429
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	430 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	431
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	432 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	433
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	434 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	435
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	436 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	437
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	438 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	439
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	440 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	441
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	442
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	443 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	444
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	445 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	446 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	447 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	448 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	449 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	450 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	451 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	452 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	453 [main] Real time: 0.070 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	454
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	455 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	456
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	457
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	458 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	459
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	460
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	461 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	462
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	463
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	464 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	465
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	466
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	467 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	468
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	469 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	470 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	471 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	472 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	473 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	474
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	475 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	476
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	477
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	478 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	479
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	480
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	481 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	482
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	483
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	484 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	485
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	486
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	487 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	488
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	489
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	490 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	491
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	492 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	493 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	494 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	495 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	496 Converted 0 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	497
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	498 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	499
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	500
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	501 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	502
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	503
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	504 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	505
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	506
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	507 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	508
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	509 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	510
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	511 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	512
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	513
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	514 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	515
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	516
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	517 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	518
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	519 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	520
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	521 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	522
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	523 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	524
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	525 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	526
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	527 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	528
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	529
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	530 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	531
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	532 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	533 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	534 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	535 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	536 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	537 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	538 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	539 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	540 [main] Real time: 0.070 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	541
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	542 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	543
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	544
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	545 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	546
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	547
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	548 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	549
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	550
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	551 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	552
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	553
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	554 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	555
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	556 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	557 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	558 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	559 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	560 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	561
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	562 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	563
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	564
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	565 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	566
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	567
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	568 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	569
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	570
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	571 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	572
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	573
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	574 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	575
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	576
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	577 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	578
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	579 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	580 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	581 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	582 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	583 Converted 0 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	584
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	585 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	586
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	587
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	588 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	589
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	590
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	591 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	592
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	593
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	594 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	595
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	596 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	597
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	598 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	599
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	600
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	601 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	602
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	603
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	604 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	605
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	606 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	607
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	608 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	609
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	610 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	611
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	612 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	613
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	614 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	615
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	616
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	617 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	618
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	619 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	620 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	621 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	622 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	623 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	624 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	625 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	626 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	627 [main] Real time: 0.071 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	628
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	629 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	630
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	631
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	632 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	633
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	634
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	635 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	636
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	637
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	638 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	639
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	640
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	641 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	642
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	643 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	644 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	645 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	646 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	647 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	648
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	649 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	650
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	651
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	652 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	653
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	654
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	655 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	656
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	657
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	658 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	659
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	660
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	661 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	662
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	663
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	664 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	665
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	666 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	667 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	668 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	669 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	670 Converted 0 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	671
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	672 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	673
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	674
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	675 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	676
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	677
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	678 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	679
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	680
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	681 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	682
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	683 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	684
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	685 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	686
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	687
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	688 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	689
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	690
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	691 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	692
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	693 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	694
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	695 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	696
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	697 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	698
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	699 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	700
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	701 ### samtools faidx reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	702
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	703
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	704 ### bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	705
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	706 [bwa_index] Pack FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	707 [bwa_index] Construct BWT for the packed sequence...
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	708 [bwa_index] 0.00 seconds elapse.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	709 [bwa_index] Update BWT... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	710 [bwa_index] Pack forward-only FASTA... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	711 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	712 [main] Version: 0.7.17-r1188
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	713 [main] CMD: bwa index reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	714 [main] Real time: 0.070 sec; CPU: 0.003 sec
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	715
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	716 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	717
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	718
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	719 ### ln -sf reference/ref.fa .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	720
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	721
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	722 ### ln -sf reference/ref.fa.fai .
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	723
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	724
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	725 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	726
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	727
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	728 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	729
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	730 READ 10 WRITTEN 2
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	731 EXCLUDED 0 EXAMINED 10
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	732 PAIRED 10 SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	733 DULPICATE PAIR 8 DUPLICATE SINGLE 0
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	734 DUPLICATE TOTAL 8
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	735
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	736 ### samtools index snps.bam
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	737
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	738
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	739 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	740
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	741
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	742 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	743
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	744
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	745 ### 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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	746
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	747
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	748 ### cp snps.filt.vcf snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	749
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	750
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	751 ### /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
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	752
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	753 Loading reference: reference/ref.fa
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	754 Loaded 1 sequences.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	755 Loading features: reference/ref.gff
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	756 Parsing variants: snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	757 Converted 1 SNPs to TAB format.
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	758
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	759 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	760
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	761
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	762 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	763
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	764
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	765 ### bcftools index -f snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	766
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	767
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	768 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	769
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	770 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	771
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	772 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	773
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	774
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	775 ### bcftools index -f snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	776
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	777
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	778 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	779
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	780 Note: the --sample option not given, applying all records regardless of the genotype
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	781
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	782 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
3bbfe41787af planemo upload commit bf653fc1bf39312caf070843fbde7b2570330917-dirty dfornika parents: diff changeset	783

Mercurial > repos > dfornika > snippy

annotate test-data/c/snps.log @ 20:3bbfe41787af draft