Irena -
I just read your question again, copied in Tommy's answer,
and this time I spotted the phrase "in order to convert the
indexed BAM file into a sorted SAM file".
Indexing only works for a sorted BAM file, if I remember
right, so you will need to sort the BAM file first, if it's
currently not sorted. When running samtools interactively
from the command line, there's an error message which says
this. So when running under a scheduler, it's worth
capturing and reading the standard error output.
Not sure if this is the problem, but it could be.
- tom blackwell -
On Sat, 14 Jan 2017, Tommy Carstensen wrote:
> Hi Irena,
>
> It should require less than 100MB of memory to index a bam file. Perhaps you
> ran into run time restrictions instead?
>
> Cheers,
> Tommy
>
> From: Irena Fischer-Hwang <[email protected]<mailto:[email protected]>>
> Date: Friday, 13 January 2017 23:16:00
> To:
> "[email protected]<mailto:[email protected]>"
>
> <[email protected]<mailto:[email protected]>>
> Subject: [Samtools-help] indexing huge BAM file
>
> Hi, I'm trying to index a huge BAM file (~180 GB) in anticipation of
> converting it to SAM. I tried running
>
>>> samtools index file.bam
>
> but it got killed, most likely because my computer ran out of RAM. Can
> someone give me a ballpark estimate of how much memory is needed to index a
> BAM file as a function of the BAM file's size? Correspondingly, what sort of
> memory requirements should I anticipate in order to convert the indexed BAM
> file to a sorted SAM file?
>
> Thanks,
> -Irena
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
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