[DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

Mon Oct 17 08:50:41 EDT 2016

Adam,

Can you post your success with Sanger workflow on

https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data

Thank you,

@bffo

--
B.F. Francis Ouellette          http://oicr.on.ca/person/francis-ouellette

On Oct 14, 2016, at 3:10 PM, Adam Struck <strucka at ohsu.edu<mailto:strucka at ohsu.edu>> wrote:

Hi Denis,

Sorry, to chime in late.  The bas file and input BAMs should be getting colocalized already (see below). Where are these files ending up when you run the workflow?

Inputs are symlinked to the OUTDIR.
https://github.com/adamstruck/CGP-Somatic-Docker/blob/develop/src/main/java/io/seqware/pancancer/CgpSomaticCore.java#L1035-L1039

Bas files are written to OUTDIR
https://github.com/adamstruck/CGP-Somatic-Docker/blob/develop/src/main/java/io/seqware/pancancer/CgpSomaticCore.java#L769-L780

I have now run 25 donors worth of data (from PRAD-UK) through this workflow using the WDL descriptor and the cromwell engine on the CCC platform without an issue.

-Adam

From: <docktesters-bounces+strucka=ohsu.edu at lists.icgc.org<mailto:docktesters-bounces+strucka=ohsu.edu at lists.icgc.org>> on behalf of Denis Yuen <Denis.Yuen at oicr.on.ca<mailto:Denis.Yuen at oicr.on.ca>>
Date: Friday, October 14, 2016 at 2:55 PM
To: Keiran Raine <kr2 at sanger.ac.uk<mailto:kr2 at sanger.ac.uk>>
Cc: "docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>" <docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>>
Subject: Re: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

Hi,

Just as a heads-up for the end-of-week in this thread.

> RUN cpanm --mirror http://cpan.metacpan.org<https://webmail.oicr.on.ca/owa/redir.aspx?REF=eiJ8sg5AzKWDmyf5Pyeos7Jkxos8aUr_J0TMU46DrwZyjUE3e_TTCAFodHRwOi8vY3Bhbi5tZXRhY3Bhbi5vcmc.> -l $OPT File::ShareDir File::ShareDir::Install Bio::Root::Version at 1.006924 Const::Fast Graph && \
     rm -rf ~/.cpanm

This got me on the right track, I actually needed the following syntax

RUN cpanm --mirror https://cpan.metacpan.org -l $OPT File::ShareDir File::ShareDir::Install CJFIELDS/BioPerl-1.6.924.tar.gz Const::Fast Graph && \

     rm -rf ~/.cpanm

However, it looks like making the suggested change breaks the workflow when attempting to run with the test data. In short, the bas file is definitely being generated inside the Docker container. Moving it to the suggested location breaks the workflow later.

I'm currently attempting to run the donor DO50311 to see if I can get more insight into what is going on.
________________________________
From: Keiran Raine [kr2 at sanger.ac.uk<mailto:kr2 at sanger.ac.uk>]
Sent: October 12, 2016 2:09 PM
To: Denis Yuen
Cc: docktesters at lists.icgc.org<mailto:docktesters at lists.icgc.org>
Subject: Re: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference
Hi Denis,

You've hit an issue that only has occurred in the last few weeks for us also.

BioPerl released a new version (first in ~20 months) that split the repository moving a whole section into a different package.

The fix would be to force the first install of BioPerl to a specific version.  Modify line 25/26 of the Dockerfile from:

RUN cpanm --mirror http://cpan.metacpan.org<x-msg://6/redir.aspx?REF=eiJ8sg5AzKWDmyf5Pyeos7Jkxos8aUr_J0TMU46DrwZyjUE3e_TTCAFodHRwOi8vY3Bhbi5tZXRhY3Bhbi5vcmc.> -l $OPT File::ShareDir File::ShareDir::Install Bio::Root::Version Const::Fast Graph && \
     rm -rf ~/.cpanm

to

RUN cpanm --mirror http://cpan.metacpan.org<x-msg://6/redir.aspx?REF=eiJ8sg5AzKWDmyf5Pyeos7Jkxos8aUr_J0TMU46DrwZyjUE3e_TTCAFodHRwOi8vY3Bhbi5tZXRhY3Bhbi5vcmc.> -l $OPT File::ShareDir File::ShareDir::Install Bio::Root::Version at 1.006924 Const::Fast Graph && \
     rm -rf ~/.cpanm

Thankfully something I could identify immediately.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2 at sanger.ac.uk<x-msg://6/redir.aspx?REF=V5Abe-SStuOqYQx5YdRisU7BV90nK9H8T6dioasb9FlyjUE3e_TTCAFtYWlsdG86a3IyQHNhbmdlci5hYy51aw..>
Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

On 12 Oct 2016, at 17:04, Denis Yuen <Denis.Yuen at oicr.on.ca<x-msg://6/redir.aspx?REF=hS48QCaXDgHI-KBBoRTpgNwsniqfzvg6l-PbcWcc7ixyjUE3e_TTCAFtYWlsdG86RGVuaXMuWXVlbkBvaWNyLm9uLmNh>> wrote:

Hi,

Keiran, I'm having trouble rebuilding the Sanger docker container in what I think is an unrelated section.
Has anything changed about the build dependencies (for example, if there is a floating version that changed over time)?
I'm attaching the build log from the Dockerfile and the log from inside the container.

________________________________
From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org<x-msg://6/redir.aspx?REF=BXOcyV55OgoSZDrIwYotXj8Er18mYWJvzzYvfp44-9xyjUE3e_TTCAFtYWlsdG86ZG9ja3Rlc3RlcnMtYm91bmNlcytkZW5pcy55dWVuPW9pY3Iub24uY2FAbGlzdHMuaWNnYy5vcmc.> [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org<x-msg://6/redir.aspx?REF=BXOcyV55OgoSZDrIwYotXj8Er18mYWJvzzYvfp44-9xyjUE3e_TTCAFtYWlsdG86ZG9ja3Rlc3RlcnMtYm91bmNlcytkZW5pcy55dWVuPW9pY3Iub24uY2FAbGlzdHMuaWNnYy5vcmc.>] on behalf of Denis Yuen [Denis.Yuen at oicr.on.ca<x-msg://6/redir.aspx?REF=hS48QCaXDgHI-KBBoRTpgNwsniqfzvg6l-PbcWcc7ixyjUE3e_TTCAFtYWlsdG86RGVuaXMuWXVlbkBvaWNyLm9uLmNh>]
Sent: October 12, 2016 10:59 AM
To: Keiran Raine
Cc: docktesters at lists.icgc.org<x-msg://6/redir.aspx?REF=5ztPaPyZn3quYjxDLHvFSLp1HBgQ1NV6NTGiMx5BNIVyjUE3e_TTCAFtYWlsdG86ZG9ja3Rlc3RlcnNAbGlzdHMuaWNnYy5vcmc.>
Subject: Re: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference
Hi,

While that would have been a good explanation, unfortunately, it doesn't seem to be the case.
In the CWL file ( https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/Dockstore.cwl<x-msg://6/UrlBlockedError.aspx> ) , the bam files are described like

inputs:

  tumor:

    type: File

    inputBinding:

      position: 1

      prefix: --tumor

    secondaryFiles:

    - .bai

  refFrom:

    type: File

    inputBinding:

      position: 3

      prefix: --refFrom

  bbFrom:

    type: File

    inputBinding:

      position: 4

      prefix: --bbFrom

  normal:

    type: File

    inputBinding:

      position: 2

      prefix: --normal

    secondaryFiles:

    - .bai

The type of File (as opposed to directory) means that while the bam and bai files are individually mounted into the docker container while it runs, the bas files never were. If Miguel has the "docker run" output from the run (should just be in the stdout of the run), we should be able to verify this by looking at what gets mounted into the container at runtime.

________________________________
From: Keiran Raine [kr2 at sanger.ac.uk<x-msg://6/redir.aspx?REF=V5Abe-SStuOqYQx5YdRisU7BV90nK9H8T6dioasb9FlyjUE3e_TTCAFtYWlsdG86a3IyQHNhbmdlci5hYy51aw..>]
Sent: October 12, 2016 10:49 AM
To: Denis Yuen
Cc: Miguel Vazquez; docktesters at lists.icgc.org<x-msg://6/redir.aspx?REF=5ztPaPyZn3quYjxDLHvFSLp1HBgQ1NV6NTGiMx5BNIVyjUE3e_TTCAFtYWlsdG86ZG9ja3Rlc3RlcnNAbGlzdHMuaWNnYy5vcmc.>
Subject: Re: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference
Hi Denis,

I expect when you unpack the the test data the BAS files exist in the archive in that area so the fact it runs the out of that step to a different location isn't detected.

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>
Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

On 12 Oct 2016, at 15:36, Denis Yuen <Denis.Yuen at oicr.on.ca<x-msg://6/UrlBlockedError.aspx>> wrote:

Hi,
I can make the modification, I'll run it through the test data and that should finish in roughly a day.
In the meantime though, I am puzzled. Why would an issue like this affect a donor dataset, but not the test data?

________________________________
From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org<x-msg://6/UrlBlockedError.aspx> [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org<x-msg://6/UrlBlockedError.aspx>] on behalf of Keiran Raine [kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>]
Sent: October 12, 2016 6:16 AM
To: Miguel Vazquez
Cc: docktesters at lists.icgc.org<x-msg://6/UrlBlockedError.aspx>
Subject: Re: [DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference
Hi,

This is assuming that it is possible to write to the location the BAM are in.

I think Denis would be best placed to make the minor modification as I don't know the process they are using for build and deploy of the images (I made modifications and then handed over for CWL).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>
Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

On 12 Oct 2016, at 10:37, Miguel Vazquez <miguel.vazquez at cnio.es<x-msg://6/UrlBlockedError.aspx>> wrote:

[The rest of the list where out of the loop for this part of the conversation, I'm putting them back in. In short, the Sanger pipeline produces the BAS file but not co-located with the BAM]
Hi Keiran,

Would it be possible then to change this and try again? what needs to happen? I guess you'll need to change the code and a new docker image be produced. Would this be our best alternative?

Miguel

On Tue, Oct 11, 2016 at 4:07 PM, Keiran Raine <kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>> wrote:
In the original version we didn't do this step, if we have write access it can be made to do that

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>
Tel:+44 (0)1223 834244 Ext: 4983<tel:%2B44%20%280%291223%20834244%20Ext%3A%204983>
Office: H104

On 11 Oct 2016, at 13:49, Miguel Vazquez <miguel.vazquez at cnio.es<x-msg://6/UrlBlockedError.aspx>> wrote:

Hi Keiran,
If the BAS and BAM files need to be collocated, why is it not created next to the BAM file?
Would it not be better if it read

private Job basFileBaseJob(int tumourCount, String sampleBam, String process, int index) {
Job thisJob = prepTimedJob(tumourCount, "basFileGenerate", process, index);

File f = new File(sampleBam);

thisJob.getCommand()

.addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")

.addArgument(installBase)

.addArgument("bam_stats")

.addArgument("-i " + sampleBam)

.addArgument("-o " + sampleBam + ".bas")

;

return thisJob;

}

Best
Miguel

On Tue, Oct 11, 2016 at 2:44 PM, Keiran Raine <kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>> wrote:
Relevant section of code:

https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/blob/develop/src/main/java/io/seqware/pancancer/CgpSomaticCore.java#L769-L780<x-msg://6/UrlBlockedError.aspx>

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>
Tel:+44 (0)1223 834244 Ext: 4983<tel:%2B44%20%280%291223%20834244%20Ext%3A%204983>
Office: H104

On 11 Oct 2016, at 13:40, Keiran Raine <kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>> wrote:

Hi,

There is a step generating the BAS files:

[2016/10/10 07:28:37] |  Running command: bash /datastore/oozie-6599f0b9-8af7-44ca-a608-03c5bbc159c6/generated-scripts/s58_basFileGenerate_control_11-runner.sh
[2016/10/10 07:28:37] |  Running command: bash /datastore/oozie-6599f0b9-8af7-44ca-a608-03c5bbc159c6/generated-scripts/s58_basFileGenerate_tumours_12-runner.sh

But if the BAM files and BAS aren't co-located then you have a problem.  You could symlink the BAM files into the work space and have all tools work from that path instead, deleting the symlinks at the end.

This is one of the changes we had to implement differently as the BAS file data was being held in the GNOS xml data structures during the initial processing.  Moving to this means that any BAM input is sufficient.

Hope this is easier to solve now,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2 at sanger.ac.uk<x-msg://6/UrlBlockedError.aspx>
Tel:+44 (0)1223 834244 Ext: 4983<tel:%2B44%20%280%291223%20834244%20Ext%3A%204983>
Office: H104

On 11 Oct 2016, at 13:31, Miguel Vazquez <miguel.vazquez at cnio.es<x-msg://6/UrlBlockedError.aspx>> wrote:

Keiran,
Its downloading the files still but in fact it does not seem to download any BAS file. Could you please educate me a bit on what are these and how I can create them?
Best
Miguel

On Tue, Oct 11, 2016 at 2:22 PM, Miguel Vazquez <miguel.vazquez at cnio.es<x-msg://6/UrlBlockedError.aspx>> wrote:

4. It looks like the *_pindel_input_* steps run for only 22-23 seconds which could indicate a problem with either the headers or the absence of the BAS file from the expected location.

I think that you just revealed the problem. There is in fact no BAS files only BAM and BAI. There where BAS files for the test data HCC1143 which is the one that in fact work. It seems like BAS files are not gathered by gnos, could that be? or that my script fails to copy them. I'll try to gather a different sample with my client and check.
Not knowing a thing about these files explains why I didn't notice. I'll get back to you when I know more.
Best
Miguel

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
<build.log><outer.build.log>

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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