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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Hi Chris,

as a workaround, can you try to set: retry_metadata_internally = False

Cheers, Bjoern

Am 09.06.2015 um 20:41 schrieb C. Ch.:

Hi Bjoern, 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. Cheers,Cristian

...

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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