Hello Hong,

There is likely a problem with the formatting of your input file. BED and GFF format are very different, and this may be the problem. You will want to input a strict "BED6" file to this tool:


http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed

http://wiki.g2.bx.psu.edu/Learn/Datatypes#GFF

If you continue to have problems, please submit a bug report by clicking on the green bug icon for the red error dataset. This allows us to access your data/job privately and provide help/feedback.

Best,

Jen
Galaxy team

On Apr 3, 2012, at 4:37 PM, xu hong wrote:

Hi Anton,

I'm a biological student using Galaxy sever to fetch sequences in
fasta format for our bioinformatics data analysis. First, I uploaded
our BED file(I think there is no significant difference from the GFF
format defined in Galaxy/UCSC), and then use "Fetch Sequences"
function in Galaxy Server.
However, I got the following error:

"2: Extract Genomic DNA on data 1
0 bytes
An error occurred running this job: Traceback (most recent call last):
File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py",
line 288, in<module>
f __name__ == "__main__": __main__()
File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py"
"

Could you help me configure out what's wrong with my analysis or could
you get the fasta file I want for me?

Attached is the BED file(based on hg18) I uploaded to Galaxy server in psu.

Thanks.

Beg your reply.

Best
Hong Xu
Zhejiang University,China
<IGGPart2.rar>


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