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BOWTIE PE #15

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
...BOWTIE PE is still running ..from one week! No errors, seems that there are 
no progress in the output stream. I attach it. The input reads are the same I 
used for the other modules: did you have the same strange behavior?

Federica

Original issue reported on code.google.com by federica...@gmail.com on 9 Aug 2011 at 11:17

Attachments:

GoogleCodeExporter commented 9 years ago 
If I remember correctly, Bowtie takes at most a few hours to complete. Is it 
stuck on the Index or Alignment module?  

Sam

Original comment by shobe...@gmail.com on 10 Aug 2011 at 6:28

GoogleCodeExporter commented 9 years ago 
That's true. it is stuck on the alignment module...I agree that is not 
realistic this running time given the few reads of the input files I used for 
the testing.

Fed

Original comment by federica...@gmail.com on 10 Aug 2011 at 6:42

GoogleCodeExporter commented 9 years ago 
I would try restarting just the alignment module (right click it and click 
'restart module'). In the meantime, I'll look into possible reasons for this 
hangup. 

Sam

Original comment by shobe...@gmail.com on 10 Aug 2011 at 6:54

GoogleCodeExporter commented 9 years ago 
I have already restarted it yesterday night...will tell you how it 
goes...thanks!

Original comment by federica...@gmail.com on 10 Aug 2011 at 7:05

GoogleCodeExporter commented 9 years ago 
Hi, the module is still running after the whole  we..I think there si for sure 
somehting weird bc BOWTIE is super fast, and the input is so small...I don't 
have any guess about that bc the SE run went so smooth...

Fed

Original comment by federica...@gmail.com on 15 Aug 2011 at 7:47

GoogleCodeExporter commented 9 years ago 
I disabled the verbose option in the "Bowtie: Alignment" module and it 
completed in only 1 minute (after the 3 hours indexing module). Here is the 
output file:
/projects1/test_pipeline/NEW_ORGANIZATION/Aligners/BOWTIE_SWITCH/testbowtie_pe.s
am

If this file looks good then it seems disabling this parameter is a possible 
solution to the hanging problem.

Original comment by shobe...@gmail.com on 22 Aug 2011 at 6:58

GoogleCodeExporter commented 9 years ago 
Wow, perfect the file looks good!  Can you please copy the final .pipe you have 
used (the working one) into /projects2/ServerLibrary/Aligners/PE? SO I am sure 
we have the definitive there.
 thanks! Probably this option was charging the pipeline too much?

Fed

Original comment by federica...@gmail.com on 26 Aug 2011 at 8:00

GoogleCodeExporter commented 9 years ago 
Yeah it's hard to say exactly why it causes such a problem. It could just be a 
bug within the program. But considering that when it works correctly, it turns 
a 1 minute run into a 1 hour run, it's safe to say that it's a very bad option. 

I copied the working pipe file to 
/projects2/ServerLibrary/Aligners/PE/Bowtie_PE.pipe

Sam

Original comment by shobe...@gmail.com on 26 Aug 2011 at 9:30