Closed msubirana closed 4 years ago
I get this error
sambamba-sort: Cannot open or create file '/imppc/labs/lplab/share/marc/insulinomas/processed/bam/hg38/bwa/Sambamba/sambamba-pid14901-xxib/stdin.339' : Too many open files
Running
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 --tmpdir ${outPath} \ sambamba index -t $cores ${outPath}/${filename}.bam
The fq.gz files are about 30gb (being paired-end)
That is a systems setting. You can try to increase -m memory limit to reduce chunks. Also test without pipes.
I get this error
Running
The fq.gz files are about 30gb (being paired-end)