Hi Omri,

Thanks for reporting this issue.  There were two different FASTQ to FASTA tools loaded in Galaxy.  The one located under the 'Convert Formats' tool menu was only designed to handle Solexa formatted FASTQ files, which was different from the tool located under 'NGS: QC and manipulation' --> 'Generic FASTQ manipulation' --> 'FASTQ to FASTA converter' which works on any FASTQ variant.  Sorry for this confusion, we've made the tool which works on any variant the default tool in both locations.  

You can use the tool that is now present in either location to convert your file to FASTA.  Unfortunately, in this case, the re-run button will not work and you will have to manually re-select the tool from the left-hand menu.

Thanks for using Galaxy,

Dan



On Jun 9, 2010, at 12:45 PM, Omri Finkel wrote:

Hi Dan,

Thank you for your response. I clicked the bug link (green on my screen..) and sent out the report. I can share my workflow, but all I have done with this particular file was upload it and then try to convert it. 

Here is the error message:
An error occurred running this job: fastq_to_fasta: Invalid quality score value (char '/' ord 47 quality value -17) on line 12

gzip: stdout: Broken pipe


Cheers,

Omri

On Wed, Jun 9, 2010 at 7:29 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:
Hi Omri,


Can you provide an example of how this is not working? If you received a job error (red dataset) can you click on the blue bug link for that dataset and report the error? Or you can share your history with us and we can take a look.


Thanks for using Galaxy,

Dan


On Jun 9, 2010, at 6:20 AM, Omri Finkel wrote:

Hello, I've been trying to convert a 454 metagenomic dataset I've downloaded from genbank SRA database, from FASTQ to FASTA. 
The operation doesn't seem to work on the Galaxy web interface. 

Help?

thanks,

Omri

--
Omri Finkel
The Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Givat Ram 91904
tel: 02-6584862
e-mail: omri.finkel@mail.huji.ac.il


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--
Omri Finkel
The Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Givat Ram 91904
tel: 02-6584862
e-mail: omri.finkel@mail.huji.ac.il