[DOCKTESTERS] - Crick
Denis Yuen
Denis.Yuen at oicr.on.ca
Tue Jan 10 10:22:38 EST 2017
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
Ontario Institute for Cancer Research
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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
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Jonas Demeulemeester, PhD
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