Yes, those are the intermediate temporary files - assuming samtools sort finished successfully they will automatically be deleted once the combined file is produced.
New versions of samtools like you use -T to specify the prefix of the temporary files explicitly. Peter On Tue, Nov 25, 2014 at 10:39 AM, john@home <john.groenend...@upcmail.nl> wrote: > Hi Peter > > The sort command runs (slowly) but seperate files are created; > Nr32.sorted.0000.bam > Nr32.sorted.0001.bam > etc > > Kind regards, > Vriendelijke groeten, > John > > > -----Oorspronkelijk bericht----- > Van: Peter Cock [mailto:p.j.a.c...@googlemail.com] > Verzonden: dinsdag 25 november 2014 10:12 > Aan: john@home > CC: samtools-help@lists.sourceforge.net > Onderwerp: Re: [Samtools-help] sort command > > On Tue, Nov 25, 2014 at 8:53 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! > > You probably want to run this command (with no greater than signs): > > samtools sort Nr32.bam Nr32.sorted > > That means Nr32.bam is the input BAM file, and Nr32.sorted is the prefix for > the sorted output. This will create Nr32.sorted.bam for you. > > Peter > ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
