Question: samtools sort failed to merge tmp .bam file
0
gravatar for johnnytam100
20 months ago by
johnnytam100100
johnnytam100100 wrote:

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.

bwa samtools bam • 1.5k views
ADD COMMENTlink written 20 months ago by johnnytam100100
2

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by genomax70k

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

ADD REPLYlink written 8 months ago by rse90
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