Sigh. Of course it was going to be something trivial. Thanks for the help.
A minor other point, it seems samtools goes above the requested memory by a
non-negligible amount. I was already accounting for the memory needed by
basic system processes, by asking samtools to use 0.5G less than the
available RAM. But even so, it ends up exceeding available RAM and the
process aborts with "Killed". Not a big deal. I'll just give it even more
of a buffer.
Thanks again.
On Wed, Mar 11, 2015 at 1:03 AM, Colin Hercus <co...@novocraft.com> wrote:
> The problem is the decimal point in the -m setting -m 1.75G. The code will
> pick this up as a request for 1 byte of RAM.
>
> The help for -m is ..
>
> -m INT where INT stands for integer.
>
> so try -m 1750M
>
> On 11 March 2015 at 10:24, 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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