Dear all,
When I am running samtools to sort BAM files by read names, sometimes
samtools will give a truncated output file without warning. Most of the
output files seems to have the expected file size. Therefore I suspect
the truncation may be due to out of memory kill by the kernel, due to
the server being under heavy load when samtools is running. I am unable
to check the log file to verify whether it is indeed an OOM issue due to
the lack of admin right.
My question is that, how will samtools behave when it is running out of
memory? Will it give a warning, instead of just producing a truncated
output file? Or is this truncation due to other issues not related to
memory?
I am using the basic command 'samtools sort -n $f ${f/.bam/.sorted}' in
a for loop. The BAM files have an average size of 500-600 MB, with about
4 million reads.
The samtools version that gave this problem is either 0.1.17 or 0.1.18.
I have tried version 1.1, but I am unable to replicate the problem
(probably because the server was not under heavy load).
Many thanks,
Chee
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