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

[Keiran Raine]

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
Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

> On 11 Oct 2016, at 13:31, Miguel Vazquez <miguel.vazquez at cnio.es> 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 <mailto:miguel.vazquez at cnio.es>> 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
> 




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