Mercurial > repos > simon-gladman > snippy

diff 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
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--- a/test-data/test/snps.log	Tue Jul 07 20:50:21 2015 -0400
+++ b/test-data/test/snps.log	Tue Jul 07 21:20:06 2015 -0400
@@ -4,58 +4,30 @@
 
 ### bwa index reference/ref.fa
 
-[bwa_index] Pack FASTA... 0.05 sec
+[bwa_index] Pack FASTA... 0.04 sec
 [bwa_index] Construct BWT for the packed sequence...
-[bwa_index] 2.38 seconds elapse.
-[bwa_index] Update BWT... 0.03 sec
+[bwa_index] 2.34 seconds elapse.
+[bwa_index] Update BWT... 0.04 sec
 [bwa_index] Pack forward-only FASTA... 0.03 sec
-[bwa_index] Construct SA from BWT and Occ... 0.68 sec
+[bwa_index] Construct SA from BWT and Occ... 0.61 sec
 [main] Version: 0.7.12-r1039
 [main] CMD: bwa index reference/ref.fa
-[main] Real time: 3.202 sec; CPU: 3.166 sec
+[main] Real time: 3.079 sec; CPU: 3.060 sec
 
-### (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)
+### (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)
 
 [samfaipath] fail to read file ref.fa.
-[M::mem_pestat] analyzing insert size distribution for orientation FF...
-[M::mem_pestat] (25, 50, 75) percentile: (8628, 8676, 9466)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (6952, 11142)
-[M::mem_pestat] mean and std.dev: (8916.09, 391.80)
-[M::mem_pestat] low and high boundaries for proper pairs: (6114, 11980)
-[M::mem_pestat] analyzing insert size distribution for orientation FR...
-[M::mem_pestat] (25, 50, 75) percentile: (419, 472, 524)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (209, 734)
-[M::mem_pestat] mean and std.dev: (469.19, 77.94)
-[M::mem_pestat] low and high boundaries for proper pairs: (104, 839)
-[M::mem_pestat] analyzing insert size distribution for orientation RF...
-[M::mem_pestat] (25, 50, 75) percentile: (980, 980, 1021)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (898, 1103)
-[M::mem_pestat] mean and std.dev: (998.83, 26.54)
-[M::mem_pestat] low and high boundaries for proper pairs: (857, 1144)
-[M::mem_pestat] analyzing insert size distribution for orientation RR...
-[M::mem_pestat] (25, 50, 75) percentile: (8665, 8710, 9466)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (7063, 11068)
-[M::mem_pestat] mean and std.dev: (9008.68, 396.07)
-[M::mem_pestat] low and high boundaries for proper pairs: (6262, 11869)
-[M::mem_pestat] skip orientation FF
-[M::mem_pestat] skip orientation RF
-[M::mem_pestat] skip orientation RR
 [M::mem_pestat] skip orientation FF as there are not enough pairs
 [M::mem_pestat] analyzing insert size distribution for orientation FR...
-[M::mem_pestat] (25, 50, 75) percentile: (416, 471, 524)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (200, 740)
-[M::mem_pestat] mean and std.dev: (468.25, 78.99)
-[M::mem_pestat] low and high boundaries for proper pairs: (92, 848)
-[M::mem_pestat] analyzing insert size distribution for orientation RF...
-[M::mem_pestat] (25, 50, 75) percentile: (980, 1023, 1044)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (852, 1172)
-[M::mem_pestat] mean and std.dev: (1014.73, 29.27)
-[M::mem_pestat] low and high boundaries for proper pairs: (788, 1236)
+[M::mem_pestat] (25, 50, 75) percentile: (429, 488, 536)
+[M::mem_pestat] low and high boundaries for computing mean and std.dev: (215, 750)
+[M::mem_pestat] mean and std.dev: (479.53, 81.93)
+[M::mem_pestat] low and high boundaries for proper pairs: (108, 857)
+[M::mem_pestat] skip orientation RF as there are not enough pairs
 [M::mem_pestat] skip orientation RR as there are not enough pairs
-[M::mem_pestat] skip orientation RF
 [main] Version: 0.7.12-r1039
-[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
-[main] Real time: 31.742 sec; CPU: 112.767 sec
+[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
+[main] Real time: 0.268 sec; CPU: 0.262 sec
 
 ### samtools index snps.bam
 
@@ -66,28 +38,12 @@
 ### tabix -s 1 -b 2 -e 2 snps.depth.gz
 
 
-### fasta_generate_regions.py reference/ref.fa.fai 174692 > reference/ref.txt
+### fasta_generate_regions.py reference/ref.fa.fai 1397543 > reference/ref.txt
 
 
-### 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
+### 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
 
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:0..174692
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:174692..349384
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:524076..698768
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:698768..873460
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:873460..1048152
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1048152..1222844
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397536..1572228
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1572228..1746920
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1746920..1921612
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:2445688..2620380
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:2620380..2795072
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:2795072..2969764
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:3493840..3668532
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:3668532..3843224
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:3843224..4017916
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:5240760..5415452
-WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:5415452..5498450
+WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397543..2795086
 
 ### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf
 
@@ -104,7 +60,7 @@
 Loaded 1 sequences.
 Loading features: reference/ref.gff
 Parsing variants: snps.vcf
-Converted 12216 SNPs to TAB format.
+Converted 0 SNPs to TAB format.
 
 ### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa