Mercurial > repos > simon-gladman > snippy

annotate test-data/test/snps.log @ 0:da9e55d788b8 draft

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