+ ACC=AF086833 + mkdir -p refs + REF=refs/AF086833.fa + BAM=align.bam + bio fetch -format fasta AF086833 + bwa index refs/AF086833.fa + samtools faidx refs/AF086833.fa + R1=read1.fq + R2=read2.fq + pywgsim -N 10000 refs/AF086833.fa read1.fq read2.fq + bwa mem refs/AF086833.fa read1.fq read2.fq + samtools sort + samtools index align.bam + freebayes -C 10 -f refs/AF086833.fa align.bam