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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