More tests show that setting only -m leads to the same problem, but setting
only -@ works fine. Also, I believe there is no problem on a normal server.
We see the problematic behavior only on AWS instances.
On Tue, Mar 10, 2015 at 10:24 PM, Ashish Agarwal <agarwal1...@gmail.com>
wrote:
> 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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