Bioinformatics Data Analysis
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Run Parameters
Parameters used during the run:
  • Genome accession number: AF086833
  • The NCBI project run number: PRJNA257197
  • How many samples to process: 5

Result description.

Output Messages
Messages printed to the standard output stream:


        
Other Messages
Messages printed to the standard error stream:
+ ID=PRJNA257197
+ ACC=AF086833
+ N=5
+ mkdir -p refs
+ REF=refs/AF086833.fa
+ efetch -db nuccore -id AF086833 -format fasta
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ efetch -format runinfo
+ esearch -db sra -query PRJNA257197
+ cat runinfo.csv
+ grep SRR
+ cut -f 1 -d ,
+ head -5
+ mkdir -p reads
+ LIMIT=100000
+ cat srr.txt
+ parallel 'fastq-dump -X 100000 -O reads --split-files {} >> log.txt'
+ mkdir -p bam
+ cat srr.txt
+ parallel 'bwa mem refs/AF086833.fa reads/{}_1.fastq reads/{}_2.fastq 2>> log.txt | samtools sort > bam/{}.bam 2>> log.txt'
+ cat srr.txt
+ parallel 'samtools index bam/{}.bam 2>> log.txt'
+ bcftools call --ploidy 1 -vm -Ou
+ bcftools mpileup -Ou -f refs/AF086833.fa bam/SRR1972917.bam bam/SRR1972918.bam bam/SRR1972919.bam bam/SRR1972920.bam bam/SRR1972921.bam
+ bcftools norm -Ov -f refs/AF086833.fa -d all -
Lines   total/split/realigned/skipped:	576/0/0/0

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