[DOCKTESTERS] - Crick

[Jonas Demeulemeester]

Hi Denis,

I only have the output from my screen session (attached).
This was a test run with the DO218695 donor.

I’ll also try running again to get you the full logs or to see where I went wrong myself.

Cheers,
Jonas


_________________________________
Jonas Demeulemeester, PhD
Postdoctoral Researcher
The Francis Crick Institute
1 Midland Road
London
NW1 1AT

T: +44 (0)20 3796 2594
M: +44 (0)7482 070730
E: jonas.demeulemeester at crick.ac.uk
W: www.crick.ac.uk



On 10 Jan 2017, at 15:22, Denis Yuen <Denis.Yuen at oicr.on.ca<mailto: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

Ontario Institute for Cancer Research
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From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org<mailto:docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org> [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org<mailto:docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org>] on behalf of Jonas Demeulemeester [Jonas.Demeulemeester at crick.ac.uk<mailto:Jonas.Demeulemeester at crick.ac.uk>]
Sent: January 10, 2017 5:55 AM
To: docktesters at lists.icgc.org<mailto: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
1 Midland Road
London
NW1 1AT

T: +44 (0)20 3796 2594
M: +44 (0)7482 070730
E: jonas.demeulemeester at crick.ac.uk
W: www.crick.ac.uk



The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT


The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
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