Results generated by running the recipe.
Parameters used during the run:
*** BOWTIE2 SE flagstat: 10000 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 6372 + 0 mapped (63.72% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) *** BWA SE flagstat: 10351 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 351 + 0 supplementary 0 + 0 duplicates 7571 + 0 mapped (73.14% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) *** BOWTIE2 PE flagstat: 20000 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 12537 + 0 mapped (62.69% : N/A) 20000 + 0 paired in sequencing 10000 + 0 read1 10000 + 0 read2 9828 + 0 properly paired (49.14% : N/A) 11482 + 0 with itself and mate mapped 1055 + 0 singletons (5.27% : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) *** BWA PE flagstat: 20740 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 740 + 0 supplementary 0 + 0 duplicates 15279 + 0 mapped (73.67% : N/A) 20000 + 0 paired in sequencing 10000 + 0 read1 10000 + 0 read2 14480 + 0 properly paired (72.40% : N/A) 14528 + 0 with itself and mate mapped 11 + 0 singletons (0.05% : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
+ 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