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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