As long as it finished creating all of the temporary files then you can
simply run "samtools merge" yourself. BTW, make sure that you haven't run
out of room on the drive. That's a likely cause of this problem.
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<devon.r...@dzne.de>
On Sat, Jan 17, 2015 at 4:53 PM, VlLADISLAV BIRYUKOV <magic-zo...@mail.ru>
wrote:
> Hello!!
>
> I have one problem with samtools sort. My unsorted bam file is *193 Gb*
> size, and when I tried to sort it, program creates thousands temporary
> files, but doesn't merge them.
> I'm waited, but in list of processes samtools sort finished its job.
>
> I launch it with *samtools sort my_unsorted_bam_file.bam sorted_result*
>
> Please, give me advice how to solve this problem. Maybe problem with
> command for launching. Prompt me, how use other options with memory (I can
> use *20 threads*)
>
> Thanks!
>
>
>
> ------------------------------------------------------------------------------
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------------------------------------------------------------------------------
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet
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