Mercurial > repos > simon-gladman > snippy
comparison test-data/test/snps.log @ 0:0801bffdfcc8 draft
Initial upload
| author | simon-gladman |
|---|---|
| date | Sun, 05 Jun 2016 21:12:39 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:0801bffdfcc8 |
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| 1 | |
| 2 ### samtools faidx reference/ref.fa | |
| 3 | |
| 4 | |
| 5 ### bwa index reference/ref.fa | |
| 6 | |
| 7 [bwa_index] Pack FASTA... 0.04 sec | |
| 8 [bwa_index] Construct BWT for the packed sequence... | |
| 9 [bwa_index] 2.34 seconds elapse. | |
| 10 [bwa_index] Update BWT... 0.04 sec | |
| 11 [bwa_index] Pack forward-only FASTA... 0.03 sec | |
| 12 [bwa_index] Construct SA from BWT and Occ... 0.61 sec | |
| 13 [main] Version: 0.7.12-r1039 | |
| 14 [main] CMD: bwa index reference/ref.fa | |
| 15 [main] Real time: 3.079 sec; CPU: 3.060 sec | |
| 16 | |
| 17 ### (bwa mem -v 2 -M -R '@RG ID:snps SM:snps' -t 1 reference/ref.fa /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_1.fq /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_2.fq | samtools view -@ 1 -q 60 -F 3844 -S -b -u -T ref.fa - | samtools sort -@ 1 - snps) | |
| 18 | |
| 19 [samfaipath] fail to read file ref.fa. | |
| 20 [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| 21 [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| 22 [M::mem_pestat] (25, 50, 75) percentile: (429, 488, 536) | |
| 23 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (215, 750) | |
| 24 [M::mem_pestat] mean and std.dev: (479.53, 81.93) | |
| 25 [M::mem_pestat] low and high boundaries for proper pairs: (108, 857) | |
| 26 [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| 27 [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| 28 [main] Version: 0.7.12-r1039 | |
| 29 [main] CMD: bwa mem -v 2 -M -R @RG ID:snps SM:snps -t 1 reference/ref.fa /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_1.fq /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_2.fq | |
| 30 [main] Real time: 0.268 sec; CPU: 0.262 sec | |
| 31 | |
| 32 ### samtools index snps.bam | |
| 33 | |
| 34 | |
| 35 ### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz | |
| 36 | |
| 37 | |
| 38 ### tabix -s 1 -b 2 -e 2 snps.depth.gz | |
| 39 | |
| 40 | |
| 41 ### fasta_generate_regions.py reference/ref.fa.fai 1397543 > reference/ref.txt | |
| 42 | |
| 43 | |
| 44 ### freebayes-parallel reference/ref.txt 1 -p 1 -q 20 -m 60 -F 0.9 -C 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf | |
| 45 | |
| 46 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397543..2795086 | |
| 47 | |
| 48 ### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf | |
| 49 | |
| 50 | |
| 51 ### bgzip -c snps.vcf > snps.vcf.gz | |
| 52 | |
| 53 | |
| 54 ### tabix -p vcf snps.vcf.gz | |
| 55 | |
| 56 | |
| 57 ### /usr/local/Cellar/snippy/2.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab | |
| 58 | |
| 59 Loading reference: reference/ref.fa | |
| 60 Loaded 1 sequences. | |
| 61 Loading features: reference/ref.gff | |
| 62 Parsing variants: snps.vcf | |
| 63 Converted 0 SNPs to TAB format. | |
| 64 | |
| 65 ### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa | |
| 66 |