Hi John,
Yes, you told it to run single threaded, so it'll take a while to sort a
large input (try the -@ option). Those files are temporary files that will
eventually be merged together and then removed before samtools finishes.
Ignore them.
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 Tue, Nov 25, 2014 at 11:19 AM, john@home <john.groenend...@upcmail.nl>
wrote:
> Hi Devon,
>
>
>
> The sort command runs (slowly) but seperate files are created;
>
> Nr32.sorted.0000.bam
>
> Nr32.sorted.0001.bam
>
> etc
>
>
>
> Vriendelijke groeten,
>
> John
>
>
>
>
>
>
>
> *Van:* dprya...@gmail.com [mailto:dprya...@gmail.com] *Namens *Devon Ryan
> *Verzonden:* dinsdag 25 november 2014 9:54
> *Aan:* john@home
> *CC:* samtools-help@lists.sourceforge.net
> *Onderwerp:* Re: [Samtools-help] question about sort
>
>
>
> Hi John,
>
>
> The output file wasn't created because, as the error message stated, you
> need to specify an output name prefix:
>
>
> samtools sort Nr32.bam Nr32.sorted
>
>
>
> Best,
> 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
>
>
>
> On Tue, Nov 25, 2014 at 9:28 AM, john@home <john.groenend...@upcmail.nl>
> wrote:
>
> > Hi
>
> >
>
> > I use the command >samtools index filename.bam and nothing happens
>
> >
>
> > >samtools sort Nr32.bam
>
> > Usage samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>
>
> >
>
> > The file is exported from CLC in bam format. The file Nr32.sorted.bam is
> not created.
>
> >
>
> > Do you know what could be wromg?
>
> > Thanks!
>
> >
>
> > Kind regards,
>
>
>
>
>
>
>
>
>
>
>
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