[DOCKTESTERS] - Crick

[Miguel Vazquez]

Hi Denis,

It failed for both the test data and the one donor I tried. I don't have
the log right now, sorry. I'll run it again with test data and get it to
you in a couple of days.

On Tue, Jan 10, 2017 at 4:22 PM, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:

> Hi,
>
> For bwa-mem, do you (or Miguel) have a copy of the error message that you
> ran into?
> Also, in your case, did bwa fail with the test data (
> https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-
> Workflow/blob/2.6.8_1.2/Dockstore_cwl.json ) or was this with the
> DO218695 donor?
>
> Thanks
>
> *Denis Yuen*
> Bioinformatics Software Developer
>
>
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> *From:* docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org
> [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of
> Jonas Demeulemeester [Jonas.Demeulemeester at crick.ac.uk]
> *Sent:* January 10, 2017 5:55 AM
> *To:* docktesters at lists.icgc.org
> *Subject:* [DOCKTESTERS] - Crick
>
> Hi all,
>
> We’ve just joined in on the testing.
>
> To give you a brief overview.
> Mainly to test whether we could actually run containers locally, we’ve
> succesully run the DKFZ(+Delly) 2.0.1_cwl1.0 and Sanger 2.0.3 workflows for
> donor DO218695 (which was just one for which I had the files locally).
> The BWA-Mem 2.6.8_1.2 workflow exited with an error.
>
> We’re working on Openstack (CentOS-7.2-1604, Docker 1.12, 20 CPUs, 200GB
> RAM).
>
> I’ll get cracking on the two test donors Miguel was using (DO50311 and
> DO52140) or two others from the test 62 set if you prefer.
> Is the current main goal still to check consistency of the outputs?
> If so, I’ll send the comparison script outputs to the list and will update
> the wiki accordingly when the runs complete.
>
> Best,
> Jonas
>
> _________________________________
> Jonas Demeulemeester, PhD
> Postdoctoral Researcher
> The Francis Crick Institute
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>
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