samtools sort failed to merge tmp .bam file

Question

[johnnytam100]

I tried to sort a .bam file with the following command

/data/tam/script/bwa.kit/samtools sort libTTNRgenomemaster_map_lotusgenome.bam > libTTNRgenomemaster_map_lotusgenome.sorted.bam

The following error, together with many ...bam.tmp.XXXX.bam files were generated (XXXX up to 1491)

[bam_sort_core] merging from 1492 files...
[E::hts_open_format] fail to open file 'libTTNRgenomemaster_map_lotusgenome.bam.tmp.1020.bam'

Related threads were read but not helpful.

Any idea how to solve this problem?

Thanks.

[GenoMax]

Did you run out of space on the disk? How much memory do you have? You could try assigning more memory to sort with -m option. Post the output of ulimit -n.

[rse]

Hi, i am also having the same issue. THe output of ulimit -n is 1024 Thanks