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

planemo upload commit 4c7d4bfdccecf4acaf3ba612166182e41e5f398f-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test/snps.log	Tue Jul 07 20:45:53 2015 -0400
@@ -0,0 +1,110 @@
+
+### samtools faidx reference/ref.fa
+
+
+### bwa index reference/ref.fa
+
+[bwa_index] Pack FASTA... 0.05 sec
+[bwa_index] Construct BWT for the packed sequence...
+[bwa_index] 2.38 seconds elapse.
+[bwa_index] Update BWT... 0.03 sec
+[bwa_index] Pack forward-only FASTA... 0.03 sec
+[bwa_index] Construct SA from BWT and Occ... 0.68 sec
+[main] Version: 0.7.12-r1039
+[main] CMD: bwa index reference/ref.fa
+[main] Real time: 3.202 sec; CPU: 3.166 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)
+
+[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] 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
+
+### samtools index snps.bam
+
+
+### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz
+
+
+### tabix -s 1 -b 2 -e 2 snps.depth.gz
+
+
+### fasta_generate_regions.py reference/ref.fa.fai 174692 > 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
+
+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
+
+### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf
+
+
+### bgzip -c snps.vcf > snps.vcf.gz
+
+
+### tabix -p vcf snps.vcf.gz
+
+
+### /usr/local/Cellar/snippy/2.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
+
+Loading reference: reference/ref.fa
+Loaded 1 sequences.
+Loading features: reference/ref.gff
+Parsing variants: snps.vcf
+Converted 12216 SNPs to TAB format.
+
+### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa
+