I'm trying to run a command in parallel while piping. The reason is that the intermediate files are too big to keep, so I could discard them
I have the following codes, that do work separately:
#fixmate and convert to bam
parallel --verbose --link -j 4 'samtools fixmate -O bam,level=1 {1} /home/Teste1/samtools/unsorted/{/.}.bam -@ 8' ::: /home/Teste1/star/twopassoverhang/*.fqAligned.out.sam
#sort according to coordinate
parallel --verbose --link -j 4 'samtools sort {1} -o /home/Teste1/samtools/sorted/{/.}-sorted.bam -@ 8' ::: /home/Teste1/samtools/unsorted/*.bam
#index bam files
parallel --verbose --link -j 4 'samtools index {1} -@ 8' ::: /home/Teste1/samtools/sorted/*-sorted.bam
I've tried:
parallel --verbose --link -j 4 'samtools fixmate -O bam,level=1 {1} - -@ 4 | / #fixmate and output bam to nextcommand
samtools sort - - -@ 4 | / #sort bams
tee /home/Teste1/samtools/sorted/{/.}-sorted.bam | / #save sorted bam file to disk
samtools index - -@ 4' ::: /home/Teste1/star/twopassoverhang/*.fqAligned.out.sam #creates index
But I get the following with --dry-run:
samtools fixmate -O bam,level=1 '/homeTeste1/star/twopassoverhang/101_FRAS202421991-1a_1.fqAligned.out.sam' - -@ 4 |
samtools sort - - -@ 4 |
tee /home/Teste1/samtools/sorted/101_FRAS202421991-1a_1.fqAligned.out-sorted.bam |
samtools index - -@ 4
and running gives me:
samtools index: "-" is in a format that cannot be usefully indexed
samtools fixmate -O bam,level=1 '/home/Teste1/star/twopassoverhang/12_FRAS202372578-2r_1.fqAligned.out.sam' - -@ 4 | samtools sort - - -@ 4 | tee /home/Teste1/samtools/sorted/12_FRAS202372578-2r_1.fqAligned.out-sorted.bam | samtools index - -@ 4
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
I've tried some other variations, but without success. Any ideas?
This might work:
do_one() {
sam="$1"
sorted="$2"
#fixmate and convert to bam
samtools fixmate -O bam,level=1 "$sam" - -@ 8 |
#sort according to coordinate
samtools sort -T /home/Teste1/samtools/ - -o "$sorted" -@ 8
#index bam files
samtools index "$sorted" -@ 8
}
export -f do_one
parallel do_one {} /home/Teste1/samtools/sorted/{/.}-sorted.bam ::: /home/Teste1/star/twopassoverhang/*.fqAligned.out.sam
If you cannot get samtools
to work directly on pipes, then you might want to remove the intermediate files as soon as you are done with them:
do_one() {
sam="$1"
bam="$2"
sorted="$3"
#fixmate and convert to bam
samtools fixmate -O bam,level=1 "$sam" "$bam" -@ 8
#sort according to coordinate
samtools sort "$bam" -o "$sorted" -@ 8
#index bam files
samtools index "$sorted" -@ 8
# remove unsorted
rm "$bam"
}
export -f do_one
parallel do_one {} /home/Teste1/samtools/unsorted/{/.}.bam /home/Teste1/samtools/sorted/{/.}-sorted.bam ::: /home/Teste1/star/twopassoverhang/*.fqAligned.out.sam