On Mon, Mar 9, 2015 at 6:24 PM, Thomas W. Blackwell <tbla...@umich.edu>
wrote:
Can you give us the actual command line ?
On a node with 7.5 Gb of RAM and 4 cores, we did:
samtools sort -@ 4 -m 1.75G file.bam file_sorted > stdout 2> stderr
We've tried variations of this, such as:
samtools sort -@ 4 -m 7.00G file.bam file_sorted > stdout 2> stderr
which I suspect is wrong because it implies samtools should use 28 Gb of
RAM.
On a 16 Gb RAM node with 8 cores, we've run the analogous commands:
samtools sort -@ 8 -m 3.75G file.bam file_sorted > stdout 2> stderr
samtools sort -@ 8 -m 15.00G file.bam file_sorted > stdout 2> stderr
We've now tried with samtools 0.1.19 and 1.2, and are getting the same
behavior.
And the number of @SQ records when you do 'samtools view -H file.bam |
> egrep -e '^@SQ' | wc' ?
>
The output is:
12 36 291
Thanks for any help.
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