Re: [Samtools-help] Sort and rmdup

[Daniel S. <so...@eb...>]

Thanks for the suggestion.
Nonetheless I think I saw someone mentioning the -m is not a very 
accurate estimate?

Just a more technical question: what's the relationship between memory 
requirements and the size of the file to be sorted?
Could I infer what would be the required -m by the size of the input file?

Thanks,
Daniel

On 16/04/2010 18:20, Tom Blackwell wrote:
>
> For a quick fix, you might try using the '-m' flag to give samtools 
> sort enough memory to avoid any need for temp files. E.g.  'samtools 
> sort -m 8000000000 -o - temp.sorted | ...' for 8 Gb RAM, assuming you 
> have that much physical memory.
>
>                         -  tom blackwell  -
>
> On Fri, 16 Apr 2010, Daniel Sobral wrote:
>
>> I'm having similar problems.
>> What seems to be happening in my case is that there are for some reason
>> problems with the temp files that get created during sorting.
>>
>> Daniel
>>
>> On 16/04/2010 07:03, Henrikki Almusa wrote:
>>> Hi,
>>>
>>> I've tried to use the piping from sort but it seems to fail. If I run
>>> the two commands:
>>>
>>> samtools import ensembl-hs_GRCh37_56.fa.fai alignment-raw.sam - |
>>>    samtools sort - raw-sorted
>>> samtools rmdup raw-sorted.bam sorted.bam
>>>
>>> This produces a 1.8Gb sorted bam file. However if I try to use the
>>> piping the sort:
>>>
>>> samtools import ensembl-hs_GRCh37_56.fa.fai alignment-raw.sam - |
>>>    samtools sort -o - raw-sorted | samtools rmdup - sorted.bam
>>>
>>> I get 163 Mb bam file. What causes the difference?
>>>
>>> Thanks,
>>>
>>
>>
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