Pipe 使用GNU并行的管道命令(samtools)
我正在尝试在管道中并行运行命令。原因是中间文件太大,无法保存,因此我可以丢弃它们 我有以下代码,它们单独工作:Pipe 使用GNU并行的管道命令(samtools),pipe,gnu,gnu-parallel,samtools,Pipe,Gnu,Gnu Parallel,Samtools,我正在尝试在管道中并行运行命令。原因是中间文件太大,无法保存,因此我可以丢弃它们 我有以下代码,它们单独工作: #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.o
#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
我试过:
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
但我得到了以下结果——试运行:
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
跑步给了我:
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]
我尝试过其他一些变体,但没有成功。有什么想法吗?这可能有用:
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
如果无法让samtools
直接在管道上工作,则可能需要在完成中间文件后立即删除它们:
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