Aligners: SOAP_PE

[GoogleCodeExporter]

Hi Ivo,

The PE alignment with SOAP gave this error, and is not loading either the  
error and output stream. I attach the .pipe.

Fed 

Original issue reported on code.google.com by federica...@gmail.com on 3 Aug 2011 at 10:56

Attachments:

• [Screen shot 2011-08-03 at 3.51.32 PM.png](https://storage.googleapis.com/google-code-attachments/informatics/issue-12/comment-0/Screen shot 2011-08-03 at 3.51.32 PM.png)
• SOAP_PE_25july_UCI.pipe

[GoogleCodeExporter]

Could you try viewing the error stream in the terminal using the error log path 
/usr/pl_cache/pipeline/.../SOAPtoSAM_1_1.error at the bottom?

Sam

Original comment by shobe...@gmail.com on 8 Aug 2011 at 10:58

[GoogleCodeExporter]

The error is this one:

/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/SOAP/soap2
sam.sh: line 6: /ifshome/shobel/Bioinformatics/soap2.21/soap2sam.pl: No such 
file or directory

I checked in the script. Actually I noticed that the path to the .pl is missing 
(there was the one on cranium)...I can find the soap2sam.sh in 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/SOAP/, 
but not the .pl that is evoked in the .sh script.

DO you think that my interpretation of this error is correct?

Federica

Original comment by federica...@gmail.com on 8 Aug 2011 at 11:24

[GoogleCodeExporter]

Yes this is correct. The path called in the script is the path on cranium and 
needs to be changed to the path on fgene. But first we need to copy soap2sam.pl 
over to your server and the problem will be fixed. 

A similar problem might arise in the BWA workflow if the script wasn't changed, 
but you won't receive an error. Do you know if the paths in the bwa_sam.sh 
script were changed from /ifshome/shobel/Bioinformatics/bwa-0.5.9rc1/bwa to 
your server? 

Sam

Original comment by shobe...@gmail.com on 9 Aug 2011 at 7:03

[GoogleCodeExporter]

(1) ok, let me know when you have copied the .pl so I can test the workflow.
(2) I am actuallyusing this script: 
/projects1/test_pipeline/NEW_ORGANIZATION/scripts/bwa_sam.sh. I have modified 
it. i corrected one space and now I am runnign again the BWA PE and SE. Will 
let you know.

Fed

Original comment by federica...@gmail.com on 9 Aug 2011 at 7:16

[GoogleCodeExporter]

Ivo says he has copied over soap2sam.pl so it should be in 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/SOAP/. 

I don't have access to the modified bwa script you are using but it sounds like 
you know what you are doing. It got a bit messy trying to run single or paired 
reads along with an unknown number of options because the reads are being fed 
from the previous module instead of a data source. If you have any questions 
about it, let me know.

Sam

Original comment by shobe...@gmail.com on 9 Aug 2011 at 8:12

[GoogleCodeExporter]

Hi,

here the folder:

fgene3 
[/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/SOAP] ll
total 116
-rwxr-xr-x 1 idinov genetics  134 May  2 19:36 Queue.sh
-rwxr-xr-x 1 idinov genetics  252 Jun 16 15:40 Rwrapper.sh
-rwxr-xr-x 1 idinov genetics  511 Jun  7 16:26 Rwrapper_ifs.sh
-rwxr-xr-x 1 idinov genetics  143 May  3 16:22 ValidateSam.sh
-rwxr-xr-x 1 idinov genetics  278 Jul 19 16:40 buildstring
-rwxr-xr-x 1 idinov genetics   85 Jul 21 15:15 bwa_aln.sh
-rwxr-xr-x 1 idinov genetics 1382 Aug  5 13:21 bwa_sam.sh
-rwxr-xr-x 1 idinov genetics  137 May 12 15:58 bwaindex.sh
-rwxr-xr-x 1 idinov genetics  378 Jun  5 19:37 compliments.sh
-rwxr-xr-x 1 idinov genetics  371 Mar 29 17:37 exercise2.1.sh
-rwxr-xr-x 1 idinov genetics  627 May  6 23:25 gammaconfig.sh
-rwxr-xr-x 1 idinov genetics  456 May 26 18:53 gammacoreel.sh
-rwxr-xr-x 1 idinov genetics  385 May 26 18:11 gammacoregamma.sh
-rwxr-xr-x 1 idinov genetics  338 May  7 00:05 gammacorelatent.sh
-rwxr-xr-x 1 idinov genetics  318 May 26 18:20 gammacorelatent2.sh
-rwxr-xr-x 1 idinov genetics  318 May 26 18:35 gammacorelatent3.sh
-rwxr-xr-x 1 idinov genetics  767 May  6 21:48 gammafilelist.sh
-rwxr-xr-x 1 idinov genetics  175 Apr 13 17:31 indexing.sh
-rwxr-xr-x 1 idinov genetics   94 May 26 17:47 makecopy.sh
-rwxr-xr-x 1 idinov genetics 1249 Jul 21 13:44 maq_mapper.sh
-rwxr-xr-x 1 idinov genetics  202 Apr 22 15:35 migrate.sh
-rwxr-xr-x 1 idinov genetics  191 Jul 29 14:56 mosaikbuild.sh
-rwxr-xr-x 1 idinov genetics  207 Jul 29 14:59 mosaikbuild2.sh
-rwxr-xr-x 1 idinov genetics  302 Apr 28 13:01 msanalyser.sh
-rwxr-xr-x 1 idinov genetics  175 Jul 19 15:13 parameters.sh
-rwxr-xr-x 1 idinov genetics  118 Jun 27 16:58 soap2sam.sh
-rwxr-xr-x 1 idinov genetics  206 May  9 16:12 sortsam.sh
-rwxr-xr-x 1 idinov genetics  432 Jun 17 14:24 upload.sh
-rwxr-xr-x 1 idinov genetics  544 May 20 19:03 uploadQA.sh

..I don't see the perl. I see the .sh.

federica

Original comment by federica...@gmail.com on 9 Aug 2011 at 9:41

[GoogleCodeExporter]

Hi Federica - my bad (I confused the soap2sam.pl and soap2sam.sh files). Now 
both are here:
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/SOAP

 _ Ivo

Original comment by iwaterp...@gmail.com on 10 Aug 2011 at 6:35

• Changed state: Started

[GoogleCodeExporter]

Perfect I am running both SE and PE already.

thanks!

Original comment by federica...@gmail.com on 10 Aug 2011 at 6:52

[GoogleCodeExporter]

PERFECT! SUCCESSFUL RUN! Other two modules added in the library... :)

Original comment by federica...@gmail.com on 10 Aug 2011 at 10:07