as a workaround, can you try to set: retry_metadata_internally = False
Am 09.06.2015 um 20:41 schrieb C. Ch.:
We could default to using sorted BAM files from Bismark as that is Ok with methylkit
which we use for our downstream analysis. On the other hand we still need the unsorted BAM
files for methylation extractor which we use for visualisation.
Thanks for the reply and I'll wait for the workaround.
> Date: Mon, 8 Jun 2015 11:22:44 +0200
> From: bjoern.gruening(a)gmail.com
> To: tuto345(a)hotmail.com; galaxy-dev(a)lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Bismark doesn't end and blocks the server
> 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
> 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.
>> ___________________________________________________________ Please
>> keep all replies on the list by using "reply all" in your mail
>> client. To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at: https://lists.galaxyproject.org/
>> To search Galaxy mailing lists use the unified search at: