> Date: Mon, 8 Jun 2015 11:22:44 +0200
> From: bjoern.gruening@gmail.com
> To: tuto345@hotmail.com; galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Bismark doesn't end and blocks the server
>
> Hi,
>
> I think this is a general problem you encountered here with unsorted BAM
> files. We can reproduce it locally. Will let you know if I find a
> workaround.
>
> Cheers,
> Bjoer
>
> Am 05.06.2015 um 14:23 schrieb C. Ch.:
> > Hi all, I have a clean local install of galaxy from git (commit:
> > 40b69cb948eed2cece82a32dfc5c6116414ab97c).I've installed bismark and
> > I get an error message (see below) if I do not choose the 'sort'
> > option.I have the impression that this might be related more to
> > galaxy than to bismark itself. The result is that the server gets
> > blocked and the only solution is to restart galaxy. Any help is
> > appreciated!Cristian The error message:galaxy.datatypes.metadata
> > DEBUG 2015-06-05 11:14:12,514 setting metadata externally failed for
> > HistoryDatasetAssociation 1305: External set_meta() not
> > called[bam_index_core] the alignment is not sorted
> > (HWI-ST278R:398:C1WUTACXX:3:1101:9378:2574): 2-th chr > 1-th
> > chr[bam_index_build2] fail to index the BAM file.
> >
> >
> >
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