Hello Sebahattin,
It may be that the data is too large to run on the Galaxy public
instance, which means that a local or cloud instance would be the next
recommendation, as explained in this wiki:
http://wiki.g2.bx.psu.edu/Big%20Picture/Choices
But, before you make the investment of moving you analysis, I'd like to
offer to double check to see if there are any tool use modifications
that will allow the job to process given the resources available on Main.
What I will need is for you to send in a tool error report by clicking
on the green bug icon in the red error dataset. Please include this
email address in the comments if it is not the one you also use with
your galaxy account, so that I can link the two questions. If the tool
just gave an empty set, but not an actual error, then use Options -
Share or Publish, generate the share link, copy that and email it back
to me directly. Please note the problem datasets if not obvious and
leave all inputs and errors in an undeleted state (please undelete if
necessary) so that I can examine the entire data path that lead up to
the error.
If you want to try to troubleshoot on your own as well, some general
advice is in this part of the Support wiki:
http://wiki.g2.bx.psu.edu/Support#Error_from_tools
Hopefully we can work out a solution,
Best,
Jen
Galaxy team
On 2/14/12 4:11 AM, Sebahattin Cirak wrote:
Dear All,
I have been successful by using the online tool to align Illumina pair
end reads , each direction 5GB, and also generated a pileup of
680,000,000 lines,
but the filtering of the pileup always fails, it runs for several hours
and I get an empty file back. I tried different options and different
pileups, always the same.
Could somebody please help or what is the trick?
Thank you
Sebahattin
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