> there is no problem on a normal server. We see the problematic behavior
only on AWS instances.
I take that back. Just tried on a regular server, and we do get the problem
there too. Sorry, we've tried so many combinations of things, I'm losing
track of what worked when.
On Tue, Mar 10, 2015 at 11:15 PM, Ashish Agarwal <agarwal1...@gmail.com>
wrote:
> 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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