+ PROJECT=PRJNA257197
+ N=5
+ esearch -db sra -query PRJNA257197
+ efetch -format runinfo
+ cat runinfo.txt
+ cut -f 1 -d ,
+ grep SRR
+ head -5
+ mkdir -p reads
+ cat selected.txt
+ parallel fastq-dump -O reads -X 1000 --split-files '{}'
+ mkdir -p bam
+ cat selected.txt
+ parallel 'picard FastqToSam F1=reads/{}_1.fastq F2=reads/{}_1.fastq O=bam/{}.bam  RG=GROUP-{} LB=LIB-{} SM=SAMPLE_{} QUIET=true 2>> log.txt'
+ samtools merge -f all.bam bam/SRR1972917.bam bam/SRR1972918.bam bam/SRR1972919.bam bam/SRR1972920.bam bam/SRR1972921.bam
+ echo ''
+ echo 'SAM file header:'
+ samtools view -H all.bam
+ echo ''
+ echo 'Number of alignments with read group: GROUP-SRR1972919'
+ samtools view -c -r GROUP-SRR1972919 all.bam
+ samtools fastq -t -1 all1.fq -2 all2.fq all.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 10000 reads
+ samtools view -r GROUP-SRR1972919 all.bam
+ samtools fastq -t -1 all_SRR1972919_1.fq -2 all_SRR1972919_2fq -
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2000 reads