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VELVET SE #22

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi,

the VELVET SE ran for two days but gave this empty error stream:

/usr/pl_cache/pipeline/2011September09_15h21m18s515ms/streams/Velvetg_1_1.error

Attached the pic and the workflow.

Fed

Original issue reported on code.google.com by federica...@gmail.com on 13 Sep 2011 at 4:11

Attachments:

GoogleCodeExporter commented 9 years ago 
I think I fixed this. Try again and let me know. Thanks

Sam

Original comment by shobe...@gmail.com on 14 Sep 2011 at 12:39

GoogleCodeExporter commented 9 years ago 
Perfect, the velvet SE run went perfect already finished and with reasonable 
output data! Put it in the server library.

The Velvet PE is running from 5 days..do you think that also this module needs 
some fix? I am attaching it just to check what do you think.

Fed

Original comment by federica...@gmail.com on 15 Sep 2011 at 6:15

Attachments:

GoogleCodeExporter commented 9 years ago 
Yeah, 5 days is too long. I'll take a look.

Original comment by shobe...@gmail.com on 15 Sep 2011 at 6:21

GoogleCodeExporter commented 9 years ago 
Just to follow up...after Bernard has rebooted the system over the week end I 
ran it again (the VELVET PE) but it is running since days...I really think 
there is something weird with that given the rapidity of the assembly with the 
single end data.

Fed

Original comment by federica...@gmail.com on 19 Sep 2011 at 6:49

GoogleCodeExporter commented 9 years ago 
That is very strange. I just ran the PE on fgene1 and it completed in a few 
seconds so I'm not sure what the problem is. Which module is it stuck on for 
you? Also just a minor change - you can get rid of the "test.config" part of 
the data sink path because the module creates its own directory inside of 
/projects1/test_pipeline/NEW_ORGANIZATION/de_novo_assembly/VELVET_PE.

Original comment by shobe...@gmail.com on 19 Sep 2011 at 8:15

GoogleCodeExporter commented 9 years ago 
Actually it worked on fgene3...on fgene1 the velvetg module was stuck...I am 
using this one: are you saying that I ahve to remove the path in the output tab 
in the output data sink?

Fed

Original comment by federica...@gmail.com on 19 Sep 2011 at 9:13

Attachments:

GoogleCodeExporter commented 9 years ago 
You don't have to, but yes, if you get rid of just the last part of the path, 
the module will create an output directory in VELVET_PE instead of in 
VELVET_PE/test.config/ ("test.config" in this case is a directory).

Original comment by shobe...@gmail.com on 19 Sep 2011 at 9:18

GoogleCodeExporter commented 9 years ago 
I ran the workflow you attached on fgene1 and it worked. Is it still causing 
you problems?

Original comment by shobe...@gmail.com on 20 Sep 2011 at 12:31

GoogleCodeExporter commented 9 years ago 
No, now is ok. Thanks!

Fed

Original comment by federica...@gmail.com on 20 Sep 2011 at 12:43