Mercurial > repos > simon-gladman > snippy
comparison test-data/test/snps.log @ 0:da9e55d788b8 draft
planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty
| author | simon-gladman |
|---|---|
| date | Tue, 07 Jul 2015 20:45:53 -0400 |
| parents | |
| children | c6ecf655fde1 |
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| -1:000000000000 | 0:da9e55d788b8 |
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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... 0.05 sec | |
| 8 [bwa_index] Construct BWT for the packed sequence... | |
| 9 [bwa_index] 2.38 seconds elapse. | |
| 10 [bwa_index] Update BWT... 0.03 sec | |
| 11 [bwa_index] Pack forward-only FASTA... 0.03 sec | |
| 12 [bwa_index] Construct SA from BWT and Occ... 0.68 sec | |
| 13 [main] Version: 0.7.12-r1039 | |
| 14 [main] CMD: bwa index reference/ref.fa | |
| 15 [main] Real time: 3.202 sec; CPU: 3.166 sec | |
| 16 | |
| 17 ### (bwa mem -v 2 -M -R '@RG ID:snps SM:snps' -t 8 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 -@ 8 -q 60 -F 3844 -S -b -u -T ref.fa - | samtools sort -@ 8 - snps) | |
| 18 | |
| 19 [samfaipath] fail to read file ref.fa. | |
| 20 [M::mem_pestat] analyzing insert size distribution for orientation FF... | |
| 21 [M::mem_pestat] (25, 50, 75) percentile: (8628, 8676, 9466) | |
| 22 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (6952, 11142) | |
| 23 [M::mem_pestat] mean and std.dev: (8916.09, 391.80) | |
| 24 [M::mem_pestat] low and high boundaries for proper pairs: (6114, 11980) | |
| 25 [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| 26 [M::mem_pestat] (25, 50, 75) percentile: (419, 472, 524) | |
| 27 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (209, 734) | |
| 28 [M::mem_pestat] mean and std.dev: (469.19, 77.94) | |
| 29 [M::mem_pestat] low and high boundaries for proper pairs: (104, 839) | |
| 30 [M::mem_pestat] analyzing insert size distribution for orientation RF... | |
| 31 [M::mem_pestat] (25, 50, 75) percentile: (980, 980, 1021) | |
| 32 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (898, 1103) | |
| 33 [M::mem_pestat] mean and std.dev: (998.83, 26.54) | |
| 34 [M::mem_pestat] low and high boundaries for proper pairs: (857, 1144) | |
| 35 [M::mem_pestat] analyzing insert size distribution for orientation RR... | |
| 36 [M::mem_pestat] (25, 50, 75) percentile: (8665, 8710, 9466) | |
| 37 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (7063, 11068) | |
| 38 [M::mem_pestat] mean and std.dev: (9008.68, 396.07) | |
| 39 [M::mem_pestat] low and high boundaries for proper pairs: (6262, 11869) | |
| 40 [M::mem_pestat] skip orientation FF | |
| 41 [M::mem_pestat] skip orientation RF | |
| 42 [M::mem_pestat] skip orientation RR | |
| 43 [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| 44 [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| 45 [M::mem_pestat] (25, 50, 75) percentile: (416, 471, 524) | |
| 46 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (200, 740) | |
| 47 [M::mem_pestat] mean and std.dev: (468.25, 78.99) | |
| 48 [M::mem_pestat] low and high boundaries for proper pairs: (92, 848) | |
| 49 [M::mem_pestat] analyzing insert size distribution for orientation RF... | |
| 50 [M::mem_pestat] (25, 50, 75) percentile: (980, 1023, 1044) | |
| 51 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (852, 1172) | |
| 52 [M::mem_pestat] mean and std.dev: (1014.73, 29.27) | |
| 53 [M::mem_pestat] low and high boundaries for proper pairs: (788, 1236) | |
| 54 [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| 55 [M::mem_pestat] skip orientation RF | |
| 56 [main] Version: 0.7.12-r1039 | |
| 57 [main] CMD: bwa mem -v 2 -M -R @RG ID:snps SM:snps -t 8 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 | |
| 58 [main] Real time: 31.742 sec; CPU: 112.767 sec | |
| 59 | |
| 60 ### samtools index snps.bam | |
| 61 | |
| 62 | |
| 63 ### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz | |
| 64 | |
| 65 | |
| 66 ### tabix -s 1 -b 2 -e 2 snps.depth.gz | |
| 67 | |
| 68 | |
| 69 ### fasta_generate_regions.py reference/ref.fa.fai 174692 > reference/ref.txt | |
| 70 | |
| 71 | |
| 72 ### freebayes-parallel reference/ref.txt 8 -p 1 -q 20 -m 60 -F 0.9 -C 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf | |
| 73 | |
| 74 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:0..174692 | |
| 75 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:174692..349384 | |
| 76 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:524076..698768 | |
| 77 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:698768..873460 | |
| 78 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:873460..1048152 | |
| 79 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1048152..1222844 | |
| 80 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397536..1572228 | |
| 81 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1572228..1746920 | |
| 82 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1746920..1921612 | |
| 83 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:2445688..2620380 | |
| 84 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:2620380..2795072 | |
| 85 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:2795072..2969764 | |
| 86 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:3493840..3668532 | |
| 87 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:3668532..3843224 | |
| 88 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:3843224..4017916 | |
| 89 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:5240760..5415452 | |
| 90 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:5415452..5498450 | |
| 91 | |
| 92 ### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf | |
| 93 | |
| 94 | |
| 95 ### bgzip -c snps.vcf > snps.vcf.gz | |
| 96 | |
| 97 | |
| 98 ### tabix -p vcf snps.vcf.gz | |
| 99 | |
| 100 | |
| 101 ### /usr/local/Cellar/snippy/2.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab | |
| 102 | |
| 103 Loading reference: reference/ref.fa | |
| 104 Loaded 1 sequences. | |
| 105 Loading features: reference/ref.gff | |
| 106 Parsing variants: snps.vcf | |
| 107 Converted 12216 SNPs to TAB format. | |
| 108 | |
| 109 ### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa | |
| 110 |