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/bash
module load samtools/1.2
cd /data
ls *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