Question: samtools sort error: [bam_sort_core] merging from 3 files and 1 in-memory blocks...
0
gravatar for Joe
12 months ago by
Joe10
Vancouver
Joe10 wrote:

Hi there,

When I run script "samtools sort -n -O SAM $bamfile", an error appeared as "[bam_sort_core] merging from 3 files and 1 in-memory blocks..." and the output file is empty? I have checked the memory and it is sufficient (256G memory can be used for the 2 G file ). Anyone can help?

Joe

software error • 1.7k views
ADD COMMENTlink modified 12 months ago • written 12 months ago by Joe10
2
gravatar for genomax
12 months ago by
genomax62k
United States
genomax62k wrote:

If you are running the latest samtools then the command should be samtools sort -n -o sorted.bam input.bam (if you want file name sorted). For a 2GB file you should not need to mess with memory settings.

ADD COMMENTlink modified 12 months ago • written 12 months ago by genomax62k
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