some errors in isolated module sol2 fastq conversion

[GoogleCodeExporter]

Hi, I think this issue may be related to the one I have risen few minutes ago. 
I isolated the conversion process between solexa and fastq files as I may need 
to use it separately from  the alignment pipelines. Seems to me that the input 
and the parameters are matching. Also the scripts have always the same 
location, the output folder as well.

Sorry for the naive question, if this is the case.


Fede

Original issue reported on code.google.com by [email protected] on 20 Sep 2011 at 6:32

Attachments:

• [Screen shot 2011-09-20 at 11.25.45 AM.png](https://storage.googleapis.com/google-code-attachments/informatics/issue-26/comment-0/Screen shot 2011-09-20 at 11.25.45 AM.png)
• sol2fastq_module.pipe

[GoogleCodeExporter]

....Furthermore, if I create FROM SCRATCH the same workflow it actually works! 
SO, I s there something kinda hidden in the "pieces" of pipeline you developed? 
may it be related to the other issue I have reported (i.e. #25) when I had to 
remove a "piece" of the pipeline (as my simulated data were already in fastq)?

I attach the anonymous pipe I have created from scratch.

Federica

Original comment by [email protected] on 21 Sep 2011 at 10:08

Attachments:

• scratch.pipe

[GoogleCodeExporter]

There is nothing hidden - these workflows are the same and are both working for 
me on fgene1. Is there anything reported in the output or error streams? 

Original comment by [email protected] on 22 Sep 2011 at 8:02

[GoogleCodeExporter]

No there was anything reported ...I will try the same run on fgene1

Original comment by [email protected] on 22 Sep 2011 at 8:13

[GoogleCodeExporter]

I noticed that in your data source you are using the 150k.txt files and in the 
data sink you are naming the outputs 1k.fastq. Just wanted to make sure you you 
know that this workflow is outputting 150k.fastq files.

Original comment by [email protected] on 26 Sep 2011 at 9:37