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


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

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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