Aligners run, summary of the problems and updates: BWA SE and PE

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1) -BWA-PE: ok the run, but the file is empty:
fgene3 [/projects1/test_pipeline/NEW_ORGANIZATION/BWA_PE] ll total 0
-rw-rw-rw- 1 pipeline pipeline 0 Aug  2 18:09 samfile-0

IVO:

Please not reset the workflow. Copy the command-line executable from the 
(completed) Module-Info tab, paste it on the command line (in a standard SSH 
shell on fgene1/3) and see if there is any additional feedback indicating why 
the result would be null. I think it may be that the result is actually written 
(in some filename/location) but not copied into the user-specified partition 
(permission?) which leaves the impression of an empty result.

FED:

Done it (both for single and paired end alignment), this is what I got FOR SE:

  /projects1/test_pipeline/NEW_ORGANIZATION/scripts/bwa_sam.sh samse samfile /usr/pl_cache/pipeline/2011August03_12h07m39s584ms/Link_1.Destination-1.fasta /usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAsamsesampe_1.Output-1 /usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai -fastq /projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k.fq -
/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai
/projects1/test_pipeline/NEW_ORGANIZATION/scripts/bwa_sam.sh: line 23: [: !=: 
unary operator expected
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k
.fq -

/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k
.fq
mkdir: cannot create directory 
`/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAsamsesampe_1.Output-1': 
File exists
[bwa_sai2sam_se_core] fail to open file 
'/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai
[0]'. Abort!
/projects1/test_pipeline/NEW_ORGANIZATION/scripts/bwa_sam.sh: line 47: 16258 
Aborted                 /applications/BWA/bwa-0.5.9rc1/bwa $routine $options 
$ref $sai[0] $fastq[0] > ${outdir}/${outbase}-$i


..seems to be a writing problem?!?!?

For PE, I noticed that I haven't changed samse with sampe..I am surpr
ised that the run didn't give any error! I am running it again.

Fed

Original issue reported on code.google.com by [email protected] on 3 Aug 2011 at 10:34