Broken pipe

[msubirana]

I am using sambamba 0.6.6 in a paired-end data with the script that follows, running in a SGE cluster. bwa mem -M -t $cores \ -R "@RG\tID:${filename}\tPU:1\tSM:${filename}\tPL:ILLUMINA" \ ${ref} ${file} ${file2} | sambamba view /dev/stdin -S -f bam -t $cores | \ sambamba sort /dev/stdin -t $cores -o ${outPath}/${filename}.bam; \ sambamba index -t $cores ${outPath}/${filename}.bam

And I got the following error:

14479 Broken pipe bwa mem -M -t $cores -R "@RG\tID:${filename}\tPU:1\tSM:${filename}\tPL:ILLUMINA" ${ref} ${file} ${file2} 14480 | sambamba view /dev/stdin -S -f bam -t $cores 14481 Segmentation fault (core dumped) | sambamba sort /dev/stdin -t $cores -o ${outPath}/${filename}.bam

Bwa is starts and works, and I try the same in samtools and works perfectly. Any suggestion?

[msubirana]

I found the error, it should be: sambamba view /dev/stdin -S -f bam -t $cores | \ sambamba sort /dev/stdin -t $cores -o ${outPath}/${filename}.bam; \