PERM single end testing

[GoogleCodeExporter]

Hi,

andy and me we were starting to test also some aligner module even before the 
switch thing. I tested PERM on single end data (see attached). Evrything went 
well, the output is there, the log is correct:

"Options Info:
Reads are processed as in fastq format.
Reads with 'N' or unknown characters will be discarded.
Results for reads that map to more than 200 locations will not be reported.
The effective read length is 101.
2 mismatches are allowed in the length.
Alignments with minimum mismatches will be collected.


Info 3: Reference 
/projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa 
has 3080436076 bases.
Info 3: There are 225075736 N in the genome.
Build genome in bits  in 34 seconds.                                         
Count bucket size  in 852 seconds.                                         
Hash record  in 1303 seconds.                                         
Sort table  in 2751 seconds.                                         
Check masked loci  in 34 seconds.                                         
Info 3: Successfully made the index
Mapping 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1_F (101-bp reads) with F1 seed.
Deal read no. 37347 in 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1.fastq.
Mapping no 0 reads.
Deal read no. 37347 in 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1.fastq.
/applications/PERM/PerM0.3.3Source/perm 
/projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1.fastq -o 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/PERM_1.Outputs-1

/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1_F, Reads:, Filtered#, 153, Kept#, 37347, Mapped#, 32989, 
Multimapped#, 1184, Multimapped>200#, 88                                        

/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1_F,_ Sub0, 25662, Sub1, 5942, Sub2, 1385, 
Mapping takes in 17 seconds.                                         
Mapped single-ended long reads in 18 seconds."    

..I dont' really understand why it gives an error on the Output bc the two jobs 
9MAQSol to sanger and PERM are green and no errors, and the output have been 
written). There are no error streams.

Fed

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 6:56

Attachments:

• Alignment_PERM_UCI.pipe
• [Screen shot 2011-07-20 at 11.50.36 AM.png](https://storage.googleapis.com/google-code-attachments/informatics/issue-5/comment-0/Screen shot 2011-07-20 at 11.50.36 AM.png)

[GoogleCodeExporter]

Federica - can you please try these steps and let me know how it goes?

(1) Right-click on the failed red Data-sink of the results and select Restart 
Module? This should try to relink/provision the results into the specified 
location in the data sink.

(2) Right-click on the data-sink and select "Show Errors" what does it show?

(3) Please confirm that there are no permission restrictions on 
writing/overwriting the results in the data-sink. 

This workflow is run on fgene3 (which is also patched, Bernard emailed me), but 
I have no account and can;t see the state/results locations.

 - Ivo

Original comment by [email protected] on 20 Jul 2011 at 11:08

• Changed state: Started

[GoogleCodeExporter]

Federica - can you please try these steps and let me know how it goes? FT: My 
replie s r into the message.

(1) Right-click on the failed red Data-sink of the results and select Restart 
Module? This should try to relink/provision the results into the specified 
location in the data sink.

Done, it fails again.

(2) Right-click on the data-sink and select "Show Errors" what does it show?

See picture, nothing, blank.

(3) Please confirm that there are no permission restrictions on 
writing/overwriting the results in the data-sink. 

No eprmissions: drwxrwxrwx 2 ftorri  genetics   4096 Jul 19 16:14 
PERM_SE_results

This workflow is run on fgene3 (which is also patched, Bernard emailed me), but 
I have no account and can;t see the state/results locations.

FT: do u wanna me to try also on fgene1? Ia am using fgene3 to let fgene1 to 
andy not exhausting the fgene1 capabilities.

 - Ivo

Original comment by [email protected] on 20 Jul 2011 at 11:24

Attachments:

• [Screen shot 2011-07-20 at 4.20.35 PM.png](https://storage.googleapis.com/google-code-attachments/informatics/issue-5/comment-2/Screen shot 2011-07-20 at 4.20.35 PM.png)

[GoogleCodeExporter]

Yes, could you please run the workflow on fgene1 as well and also double check 
the entire PATH of the output files (e.g., to ensure that you can write in each 
folder from the root / up to the leaf filename.

Original comment by [email protected] on 20 Jul 2011 at 11:32

[GoogleCodeExporter]

Ok, doing it.

fed

Original comment by [email protected] on 20 Jul 2011 at 11:58

[GoogleCodeExporter]

On fgene1 it worked well as I wrote you in the email.

fed

Original comment by [email protected] on 21 Jul 2011 at 9:44