Can you give us the actual command line ? And the number of @SQ records
when you do 'samtools view -H file.bam | egrep -e '^@SQ' | wc' ?
- thanks - tom blackwell -
On Mon, 9 Mar 2015, Ashish Agarwal wrote:
> `samtools sort` is often creating millions of temp files, and google'ing
> hasn't led me to any other posts about this. Mostly people are reporting a
> problem with ~1000 files, which is resolved by using ulimit. That's not our
> issue. Our BAM files are only 1 - 3 Gb, and we have run on nodes with 8 or
> 16 Gb of RAM. We've set the -m parameter, but we still get messages like
> this to stderr:
>
> [bam_sort_core] merging from 83155297 files...
> open: Too many open files
>
> We're using samtools version 0.1.19. Has anyone seen this before?
>
> We were told by our collaborators to use version 0.1.19, but anyone have
> thoughts on using a more recent version. Are there significant differences
> between 0.1.19 and 1.2?
>
> Just to make sure, is it correct that the -m parameter takes the memory per
> thread? Or should we provide the total RAM available for all threads? The
> documentation says the former, but I want to double check since the latter
> was implied by some possibly unreliable source on the internet. (The above
> error is not affected. We've tried both.)
>
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
