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Old 09-28-2009, 10:46 AM   #190
apfejes
Senior Member
 
Location: Oakland, California

Join Date: Feb 2008
Posts: 236
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Hi ka123$,

kmcarr is right - Gerald is an intermediate program along the way from the sequencing machine to getting results. It's not an appropriate place to look for files to work with FindPeaks.

If your problem is with the sorting and pre-processing, you might consider using the s_N_sorted.txt produced by findPeaks. It's pre-sorted, so it should make your life easier.

I should also mention that the "-aligner" format used sets the format and some of the behaviours of FindPeaks. If you've selected "-aligner eland", then FindPeaks expects the files you provide to be in the Eland format. I don't know what format Gerald uses, but I'm certain it's not the same as the output from the Eland aligner.

As for the problem you're seeing, I'm not sure why 2.3M reads would cause an out of memory error, however, I suspect that despite allocating 2Gb of RAM, the machine you're using actually has less than that free. (-Xmx2G sets the maximum the application is allowed to use, not the actual amount available.) I've certainly sorted much larger files than that with the SortFiles program, although I do tend to use a machine with more than 2Gb of Ram so I don't see that problem myself.

I'm happy to try helping, but I think you need to clarify a few things for me. What aligner are you using, and what commands are you using? If we settle on one aligner, I can point you in the right direction as to the work flow you're using, and if I can see the commands you're using, I can check to see if any of the parameters should be changed.

Cheers,

Anthony
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