Mercurial > repos > simon-gladman > snippy

comparison test-data/test/snps.log @ 2:c6ecf655fde1 draft

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planemo upload commit 09dd886ffd8ab6348cb002c9383d7bf342c465a9-dirty
author simon-gladman
date Tue, 07 Jul 2015 21:20:06 -0400
parents da9e55d788b8
children
comparison
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1:a61972ea470b 2:c6ecf655fde1
2 ### samtools faidx reference/ref.fa 2 ### samtools faidx reference/ref.fa
3 3
4 4
5 ### bwa index reference/ref.fa 5 ### bwa index reference/ref.fa
6 6
7 [bwa_index] Pack FASTA... 0.05 sec 7 [bwa_index] Pack FASTA... 0.04 sec
8 [bwa_index] Construct BWT for the packed sequence... 8 [bwa_index] Construct BWT for the packed sequence...
9 [bwa_index] 2.38 seconds elapse. 9 [bwa_index] 2.34 seconds elapse.
10 [bwa_index] Update BWT... 0.03 sec 10 [bwa_index] Update BWT... 0.04 sec
11 [bwa_index] Pack forward-only FASTA... 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 12 [bwa_index] Construct SA from BWT and Occ... 0.61 sec
13 [main] Version: 0.7.12-r1039 13 [main] Version: 0.7.12-r1039
14 [main] CMD: bwa index reference/ref.fa 14 [main] CMD: bwa index reference/ref.fa
15 [main] Real time: 3.202 sec; CPU: 3.166 sec 15 [main] Real time: 3.079 sec; CPU: 3.060 sec
16 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) 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 18
19 [samfaipath] fail to read file ref.fa. 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 20 [M::mem_pestat] skip orientation FF as there are not enough pairs
44 [M::mem_pestat] analyzing insert size distribution for orientation FR... 21 [M::mem_pestat] analyzing insert size distribution for orientation FR...
45 [M::mem_pestat] (25, 50, 75) percentile: (416, 471, 524) 22 [M::mem_pestat] (25, 50, 75) percentile: (429, 488, 536)
46 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (200, 740) 23 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (215, 750)
47 [M::mem_pestat] mean and std.dev: (468.25, 78.99) 24 [M::mem_pestat] mean and std.dev: (479.53, 81.93)
48 [M::mem_pestat] low and high boundaries for proper pairs: (92, 848) 25 [M::mem_pestat] low and high boundaries for proper pairs: (108, 857)
49 [M::mem_pestat] analyzing insert size distribution for orientation RF... 26 [M::mem_pestat] skip orientation RF as there are not enough pairs
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 27 [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 28 [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 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
58 [main] Real time: 31.742 sec; CPU: 112.767 sec 30 [main] Real time: 0.268 sec; CPU: 0.262 sec
59 31
60 ### samtools index snps.bam 32 ### samtools index snps.bam
61 33
62 34
63 ### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz 35 ### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz
64 36
65 37
66 ### tabix -s 1 -b 2 -e 2 snps.depth.gz 38 ### tabix -s 1 -b 2 -e 2 snps.depth.gz
67 39
68 40
69 ### fasta_generate_regions.py reference/ref.fa.fai 174692 > reference/ref.txt 41 ### fasta_generate_regions.py reference/ref.fa.fai 1397543 > reference/ref.txt
70 42
71 43
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 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
73 45
74 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:0..174692 46 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397543..2795086
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 47
92 ### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf 48 ### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf
93 49
94 50
95 ### bgzip -c snps.vcf > snps.vcf.gz 51 ### bgzip -c snps.vcf > snps.vcf.gz
102 58
103 Loading reference: reference/ref.fa 59 Loading reference: reference/ref.fa
104 Loaded 1 sequences. 60 Loaded 1 sequences.
105 Loading features: reference/ref.gff 61 Loading features: reference/ref.gff
106 Parsing variants: snps.vcf 62 Parsing variants: snps.vcf
107 Converted 12216 SNPs to TAB format. 63 Converted 0 SNPs to TAB format.
108 64
109 ### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa 65 ### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa
110 66