+ ID=PRJNA257197
+ N=5
+ ACC=KJ660346
+ GENBANK=refs/KJ660346.gb
+ FASTA=refs/KJ660346.fa
+ GFF=refs/KJ660346.gff
+ mkdir -p refs
+ efetch -db=nuccore -format=gb -id=KJ660346
+ cat refs/KJ660346.gb
+ readseq -p -f fasta
+ cat refs/KJ660346.gb
+ readseq -p -f gff
+ grep CDS
+ bwa index refs/KJ660346.fa
+ samtools faidx refs/KJ660346.fa
+ esearch -db sra -query PRJNA257197
+ efetch -format runinfo
+ cat runinfo.csv
+ grep SRR
+ cut -f 1 -d ,
+ head -5
+ mkdir -p reads
+ LIMIT=100000
+ cat samples.txt
+ parallel 'fastq-dump -X 100000 -O reads --split-files {} >> log.txt'
+ mkdir -p bam
+ cat samples.txt
+ parallel 'bwa mem refs/KJ660346.fa reads/{}_1.fastq reads/{}_2.fastq 2>> log.txt' '|' 'samtools sort' '>' 'bam/{}.bam 2>> log.txt'
+ cat samples.txt
+ parallel 'samtools index bam/{}.bam 2>> log.txt'
+ bcftools call --ploidy 1 -vm -Ou
+ bcftools mpileup -Ou -f refs/KJ660346.fa bam/SRR1972917.bam bam/SRR1972918.bam bam/SRR1972919.bam bam/SRR1972920.bam bam/SRR1972921.bam
+ bcftools norm -Ov -f refs/KJ660346.fa -d all -
Lines   total/split/realigned/skipped:	24/0/0/0
+ cat all_variants.vcf
+ snpEff ebola_zaire -s all_effects_report.html