+ mkdir -p db
+ ACC=AF086833
+ SRR=SRR1972739
+ REF=db/AF086833.fa
+ READ1=SRR1972739_1.fastq
+ READ2=SRR1972739_2.fastq
+ efetch -db=nuccore -format=fasta -id=AF086833
+ fastq-dump -X 10000 --split-files SRR1972739
+ bowtie2-build db/AF086833.fa db/AF086833.fa
+ bwa index db/AF086833.fa
+ bowtie2 -x db/AF086833.fa -U SRR1972739_1.fastq
+ bwa mem db/AF086833.fa SRR1972739_1.fastq
+ echo '*** BOWTIE2 SE flagstat:'
+ samtools flagstat bowtie2.SE.sam
+ echo '*** BWA SE flagstat:'
+ samtools flagstat bwa.SE.sam
+ bowtie2 -x db/AF086833.fa -1 SRR1972739_1.fastq -2 SRR1972739_2.fastq
+ bwa mem db/AF086833.fa SRR1972739_1.fastq SRR1972739_2.fastq
+ echo '*** BOWTIE2 PE flagstat:'
+ samtools flagstat bowtie2.PE.sam
+ echo '*** BWA PE flagstat:'
+ samtools flagstat bwa.PE.sam