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

___________________________________________________________ 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/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support