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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
