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BWA: error in writing the sam #13

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
(1) -BWA-PE: ok the run, but the file is empty:
fgene3 [/projects1/test_pipeline/NEW_ORGANIZATION/BWA_PE] ll total 0
-rw-rw-rw- 1 pipeline pipeline 0 Aug  2 18:09 samfile-0

·       Please not reset the workflow. Copy the command-line executable from 
the (completed) Module-Info tab, paste it on the command line (in a standard 
SSH shell on fgene1/3) and see if there is any additional feedback indicating 
why the result would be null. I think it may be that the result is actually 
written (in some filename/location) but not copied into the user-specified 
partition (permission?) which leaves the impression of an empty result.

..IVO SENT ME A NEW SCRIPT, but:

Hi Ivo,

Unfortunately all the BWA runs failed again in writing the output. As you can 
see when I open up the error window, the samse and sampe process were fine 
(green and not errored). I have used the new script (that is now in: 
/projects1/test_pipeline/NEW_ORGANIZATION/scripts).

I will post also in the issues tracker.

Fed

Original issue reported on code.google.com by federica...@gmail.com on 4 Aug 2011 at 9:30

Attachments:

GoogleCodeExporter commented 9 years ago 
Hi Federica - yes, you are absolutely correct, that there was one additional 
typo that we just corrected in the "bwa_sam.sh" script. Could you please try 
the revised script and confirm this problem is resolved?

/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/SOAP and
/projects1/test_pipeline/NEW_ORGANIZATION/scripts

Thanks,

 - Ivo

Original comment by iwaterp...@gmail.com on 5 Aug 2011 at 8:48

GoogleCodeExporter commented 9 years ago 
Perfect! I am running right now the SE and PE alignemnt. Will keep you posted.

fed

Original comment by federica...@gmail.com on 8 Aug 2011 at 7:08

GoogleCodeExporter commented 9 years ago 
Hi Ivo,

I am sorry, but still with the edited script I am having the output writing 
issue. I attach both the mudles. As the previous time I have the error stream:

Unable to copy: 
src=/usr/pl_cache/pipeline/2011August09_12h14m21s364ms/BWAsamsesampe_1.Output-1,

dest=/projects1/test_pipeline/NEW_ORGANIZATION/Aligners/ALIGNERS_SWITCHED/BWA_PE

fed

Original comment by federica...@gmail.com on 11 Aug 2011 at 5:21

Attachments:

GoogleCodeExporter commented 9 years ago 
I fixed the output writing issues for these workflows. If you didn't them yet, 
you can just reset the samse/sampe modules and they will work. 

Sam

Original comment by shobe...@gmail.com on 11 Aug 2011 at 9:42

GoogleCodeExporter commented 9 years ago 
Sorry missed a word. 
If you didn't reset them yet*

Original comment by shobe...@gmail.com on 11 Aug 2011 at 9:43

GoogleCodeExporter commented 9 years ago 
I have restarted the samse/sampe.Will let you know.

fed

Original comment by federica...@gmail.com on 11 Aug 2011 at 10:18

GoogleCodeExporter commented 9 years ago 
PERFECT!!!!! they worked!!

thanks!

fed

Original comment by federica...@gmail.com on 11 Aug 2011 at 10:19