Hi Jen Thanks for your information, I'm using the public Galaxy main server and the job is yellow.It was a good point, I put the large dataset as the second input, I will wait if no success I will treat as you said.
Milad Bastami PhD student of Medical Genetics Department of Medical Genetics Shahid Beheshti's university of Medical Science
From: Jennifer Jackson jen@bx.psu.edu To: Milad Bastami mi.bastami@yahoo.com Cc: "galaxy-user@lists.bx.psu.edu" galaxy-user@lists.bx.psu.edu Sent: Tuesday, February 12, 2013 6:56 PM Subject: Re: [galaxy-user] Galaxy Join takes too long?
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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Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org