Dear all,
I run a batch job on a high-performance computing system to sort multiple SAM
files (> 600GB) and used parallel to speed up the task, but my job failed with
the following reasons:
parallel: Error: Output is incomplete. Cannot append to buffer file in
$TMPDIR. Is the disk full?parallel: Error: Change $TMPDIR with --tmpdir or use
--compress. Then I added “--compress” option and changed $TMPDIR with
“--tmpdir /scratch/$SLURM_JOBID”, but it still doesn’t work.
My job script looks like this: #!/bin/bashmodule load samtools/1.2 cd /datals
*sam* | parallel --compress --tmpdir /scratch/$SLURM_JOBID "samtools sort –T
/scratch/$SLURM_JOBID/{.} -O bam -o {}.bam {}" Could you please help me solve
this problem? Thank you in advance. Best regards,Lisa
