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annotate test-data/fna_ref_b_testing/snps.log @ 20:3bbfe41787af draft

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author dfornika
date Fri, 08 Mar 2019 20:46:56 -0500
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1 ### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
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3 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir fna_ref_b_testing --cpus 1 --ref reference.fasta --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq
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5 ### samtools faidx reference/ref.fa
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8 ### bwa index reference/ref.fa
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10 [bwa_index] Pack FASTA... 0.00 sec
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11 [bwa_index] Construct BWT for the packed sequence...
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12 [bwa_index] 0.00 seconds elapse.
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13 [bwa_index] Update BWT... 0.00 sec
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14 [bwa_index] Pack forward-only FASTA... 0.00 sec
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15 [bwa_index] Construct SA from BWT and Occ... 0.00 sec
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16 [main] Version: 0.7.17-r1188
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17 [main] CMD: bwa index reference/ref.fa
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18 [main] Real time: 0.009 sec; CPU: 0.003 sec
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20 ### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
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23 ### ln -sf reference/ref.fa .
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26 ### ln -sf reference/ref.fa.fai .
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29 ### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
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32 ### bwa mem -Y -M -R '@RG\tID:fna_ref_b_testing\tSM:fna_ref_b_testing' -t 1 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.8702. --threads 1 -m 8000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.8702. --threads 1 -m 8000M | samtools markdup -T /tmp/snippy.8702. -r -s - - > snps.bam
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34 READ 10 WRITTEN 2
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35 EXCLUDED 0 EXAMINED 10
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36 PAIRED 10 SINGLE 0
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37 DULPICATE PAIR 8 DUPLICATE SINGLE 0
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38 DUPLICATE TOTAL 8
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40 ### samtools index snps.bam
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43 ### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
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46 ### freebayes-parallel reference/ref.txt 1 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf
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49 ### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf
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52 ### cp snps.filt.vcf snps.vcf
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55 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
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57 Loading reference: reference/ref.fa
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58 Loaded 1 sequences.
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59 Loading features: reference/ref.gff
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60 Parsing variants: snps.vcf
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61 Converted 1 SNPs to TAB format.
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63 ### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
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66 ### bcftools convert -Oz -o snps.vcf.gz snps.vcf
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69 ### bcftools index -f snps.vcf.gz
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72 ### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
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74 Note: the --sample option not given, applying all records regardless of the genotype
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76 ### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
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79 ### bcftools index -f snps.subs.vcf.gz
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82 ### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
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84 Note: the --sample option not given, applying all records regardless of the genotype
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86 ### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
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