Hello Qianli,

This appears to be the same data as submitted as a recent bug? Converting the query coordinates to BED format is still the recommendation. This should be a good solution for most, if not all, of your prior Extract tool failures and is a good method overall.

First "Convert Formats -> GFF-to-BED", followed by clicking on the pencil icon to assign the last three columns on the "Edit Attributes" form, in particular you will want to get strand assigned, so that c4 = name, c5 = score, and c6 = strand. The datatype will be bed. Then extract using your custom genome and the sequence will be titled by the region coordinates.

Best,

Jen
Galaxy team

On 5/29/12 11:58 AM, Qianli Shen wrote:

Hi

I want to fetch sequence from soybean genome, according to a gff file. My gff3 file and genome file are attached to the email, because it is not easy to recongnize the format if I paste it in the email. And it keeps reporting the error:

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>
if __name__ == "__main__": __main__()
File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py"

Could you please tell me where is the problem?

Best

Qianli
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