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MAQ PE issue follow up #17

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
I noticed that I haven't reported in the tracker the MAQ PE issue.

I confirm that I have full permission on all the tree of the output folder, 
that the output has been written correctly in the cache folder and that the 
error (actually not so understandable as you were saying) is:

Unable to copy: 
src=/usr/pl_cache/pipeline/2011August09_14h30m21s353ms/SamToolsmaq2sam-long_1.Ou
tputSAMfile-1.sam, 
dest=projects1/test_pipeline/NEW_ORGANIZATION/Aligners/ALIGNERS_SWITCHED/MAQ_PE/
test.sam

Federica

Original issue reported on code.google.com by federica...@gmail.com on 10 Aug 2011 at 7:04

Attachments:

GoogleCodeExporter commented 9 years ago 
Could you attach the workflow you are using? Thanks.

Sam

Original comment by shobe...@gmail.com on 10 Aug 2011 at 7:46

GoogleCodeExporter commented 9 years ago 
Here.

Fed

Original comment by federica...@gmail.com on 10 Aug 2011 at 7:53

Attachments:

GoogleCodeExporter commented 9 years ago 
You are missing a "/" before "projects" in the destination paths. I'm pretty 
sure this is the cause of the copying problem. I'm not sure why the other one 
completed though.

Original comment by shobe...@gmail.com on 11 Aug 2011 at 10:31

GoogleCodeExporter commented 9 years ago 
Hi,

I have added the /, but I have the same error back. I confirm that I have FULL 
permission on the entire tree of the output folder.

Fed

Original comment by federica...@gmail.com on 15 Aug 2011 at 4:47

Attachments:

GoogleCodeExporter commented 9 years ago 
The fgene server admin recently gave me permission to use the server so I was 
running this workflow and the other problematic ones but it seems the server 
has been brought down? I will continue troubleshooting these problems when I 
can connect.

Original comment by shobe...@gmail.com on 16 Aug 2011 at 8:06

GoogleCodeExporter commented 9 years ago 
yes! Seems also to me..I am writing to Bernard to ask if something happened!

Original comment by federica...@gmail.com on 16 Aug 2011 at 8:28

GoogleCodeExporter commented 9 years ago 
The problem here is that maq2sam-long outputs to the standard output by 
default. Thus I believe the results are in the output stream. The workflow I 
made was running maq2sam-long from a simple script that redirects the standard 
output to the pipeline generated output file. I attached the script here. Just 
change the maq2sam-long path and make sure to give yourself permission to run 
the script.

Original comment by shobe...@gmail.com on 18 Aug 2011 at 7:04

Attachments:

GoogleCodeExporter commented 9 years ago 
Hi,

 The run went well (all is green)...I find the .map file in the output folder BUT the sam file is empty. I checked  in the cache /usr/pl_cache/pipeline/2011August18_09h40m19s951ms/, but the folder is not there anymore because the output file have been written in the designated output folder I guess. 

So given that the map file is ok, I really dont' know why it is not writing the 
sam file now...before using the script it was writing the sam file in the cache 
BUT not copying it in the output folder.

fed

Original comment by federica...@gmail.com on 18 Aug 2011 at 6:14

GoogleCodeExporter commented 9 years ago 
I'm not sure why your sam file is empty. I've run it on both cranium and fgene1 
and don't seem to be having any problems. Could you attach the workflow you 
used?

Original comment by shobe...@gmail.com on 18 Aug 2011 at 8:01

GoogleCodeExporter commented 9 years ago 
I am using this one. 

fed

Original comment by federica...@gmail.com on 18 Aug 2011 at 8:16

Attachments:

GoogleCodeExporter commented 9 years ago 
I think you just forgot to change the file path inside the script. I went ahead 
and changed it for you so it is now running:
/applications/SAMTOOLS/samtools-0.1.16/misc/maq2sam-long

Original comment by shobe...@gmail.com on 18 Aug 2011 at 8:28

GoogleCodeExporter commented 9 years ago 
No, I had to put your script in this folder 
(/projects1/test_pipeline/NEW_ORGANIZATION/scripts) bc seems I have no 
permission to write inside /applications/SAMTOOLS/samtools-0.1.16/misc/....

Fed

Original comment by federica...@gmail.com on 18 Aug 2011 at 9:11

GoogleCodeExporter commented 9 years ago 
..so /applications/SAMTOOLS/samtools-0.1.16/misc/maq2sam-long is the old one..

Fed

Original comment by federica...@gmail.com on 18 Aug 2011 at 9:12

GoogleCodeExporter commented 9 years ago 
Sorry, I'm not sure I'm following. The workflow you sent was running the 
maq2sam-long module from 
/projects1/test_pipeline/NEW_ORGANIZATION/scripts/maq2sam-long.csh. So I 
checked that script:

fgene1 [/projects1/test_pipeline/NEW_ORGANIZATION/scripts] cat maq2sam-long.csh 
#!/bin/csh
# Wrapper script to avoid ">" piepline problem
# Usage: maq2sam-long assembly.map assembly.sam
# Generates the command: maq2sam-long assembly.map > assembly.sam

date

echo "Running: maq2sam-long $1 > $2 "

/usr/local/loniWorkflows/Bioinformatics/samtools/samtools-0.1.10/maq2sam-long 
$1 > $2 

date

exit 0
--------------------------------------------------------------------------------
--

The file path was still using the cranium path so I changed that line to this:
/applications/SAMTOOLS/samtools-0.1.16/misc/maq2sam-long $1 > $2

Let me know if I'm misunderstanding something.

Original comment by shobe...@gmail.com on 18 Aug 2011 at 9:21

GoogleCodeExporter commented 9 years ago 
No, I have misunderstood. I thought you changed the path to the script in the 
pipeline edit module GUI, while you were meaning you changed the path WITHIN 
the script.
Sorry, I got it now. I am running it.

Thanks

fed

Original comment by federica...@gmail.com on 18 Aug 2011 at 9:26

GoogleCodeExporter commented 9 years ago 
Perfect! Run is ok!

fed

Original comment by federica...@gmail.com on 18 Aug 2011 at 11:41