+ 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