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1
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2 ### samtools faidx reference/ref.fa
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3
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4
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5 ### bwa index reference/ref.fa
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6
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7 [bwa_index] Pack FASTA... 0.04 sec
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8 [bwa_index] Construct BWT for the packed sequence...
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9 [bwa_index] 2.34 seconds elapse.
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10 [bwa_index] Update BWT... 0.04 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... 0.61 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: 3.079 sec; CPU: 3.060 sec
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16
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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)
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18
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19 [samfaipath] fail to read file ref.fa.
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20 [M::mem_pestat] skip orientation FF as there are not enough pairs
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21 [M::mem_pestat] analyzing insert size distribution for orientation FR...
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22 [M::mem_pestat] (25, 50, 75) percentile: (429, 488, 536)
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23 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (215, 750)
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24 [M::mem_pestat] mean and std.dev: (479.53, 81.93)
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25 [M::mem_pestat] low and high boundaries for proper pairs: (108, 857)
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26 [M::mem_pestat] skip orientation RF as there are not enough pairs
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27 [M::mem_pestat] skip orientation RR as there are not enough pairs
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28 [main] Version: 0.7.12-r1039
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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
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30 [main] Real time: 0.268 sec; CPU: 0.262 sec
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31
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32 ### samtools index snps.bam
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33
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34
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35 ### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz
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36
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37
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38 ### tabix -s 1 -b 2 -e 2 snps.depth.gz
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39
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40
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41 ### fasta_generate_regions.py reference/ref.fa.fai 1397543 > reference/ref.txt
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42
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43
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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
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45
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46 WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397543..2795086
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47
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48 ### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf
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49
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50
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51 ### bgzip -c snps.vcf > snps.vcf.gz
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52
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53
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54 ### tabix -p vcf snps.vcf.gz
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55
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56
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57 ### /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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58
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59 Loading reference: reference/ref.fa
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60 Loaded 1 sequences.
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61 Loading features: reference/ref.gff
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62 Parsing variants: snps.vcf
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63 Converted 0 SNPs to TAB format.
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64
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65 ### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa
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66
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