REAL HUMAN HIGH COVERAGE DATA-BOWTIE SE

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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 federica...@gmail.com 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