REAL HUMAN HIGH COVERAGE DATA-BOWTIE SE

[GoogleCodeExporter]

Hi, yesterday I started the testing with real human data (input: 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/full_patient_fastq/941603/94
1603_fwd.txt) but I had an error (see pic). The error stream BTW is empty:


[ftorri@fgene3 streams]$ ll
total 12
-rw-rw-rw- 1 pipeline pipeline     0 Sep 20 08:58 BowtieAlignment_1_1.error
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 20:23 BowtieAlignment_1_1.out
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 17:57 Bowtieindexing_1_1.error
-rw-rw-rw- 1 pipeline pipeline 12271 Sep 19 20:23 Bowtieindexing_1_1.out
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 17:57 
MAQSol2SangerConverter_1_1.error
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 17:57 MAQSol2SangerConverter_1_1.out


..but the process partially ran because there is a .sam file with a proper 
format:

[ftorri@fgene3 BOWTIE_SE_results]$ vi bowtie_se.sam 

I attach here the pipe. How can I diagnose the reason why the process quits? 
The other processes that were running on fgene3 are all still running...

Federica

Original issue reported on code.google.com by [email protected] on 20 Sep 2011 at 5:36

Attachments:

• [Screen shot 2011-09-20 at 10.27.40 AM.png](https://storage.googleapis.com/google-code-attachments/informatics/issue-24/comment-0/Screen shot 2011-09-20 at 10.27.40 AM.png)
• BOWTIE_SE_941603.pipe

[GoogleCodeExporter]

It is very difficult to diagnose the problem without some sort of message in 
the output or error stream. However, if this workflow completes with smaller 
data sets it is likely that the 152GB input file is causing memory issues.

Original comment by [email protected] on 22 Sep 2011 at 8:18