Hello Milad,

I am not sure if you are using the public Galaxy Main server (https://main.g2.bx.psu.edu) or your own local computer, or if the jobs are yellow and running or still grey and in the waiting-to-run stage.

If using Galaxy Main, and if actually running (dataset is yellow), this type of job sometimes can take a while to run on very large datasets.

To improve the chances of a successful run and to increase the speed of any run, make sure to put the large dataset as the first input and the smaller file as the second input. The interval operations tools use an indexing strategy where the second input file is the portion loaded memory and the first file is processed against it.

Hopefully this helps,

Jen
Galaxy team

On 2/12/13 2:58 AM, Milad Bastami wrote:

I'm trying to joint two large intervals (one with 800,000 intervals and the other with about 350,000 intervals) using operates on intervals > join tool . I have no idea how long it should takes normaly. Two days have past and it is still runnig. Is there any limitation in file size for this tool?

Any help would be appreciated.

Regards,

Milad Bastami

PhD student of Medical Genetics

Department of Medical Genetics

Shahid Beheshti's university of Medical Science
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