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Old 02-11-2015, 05:30 AM   #1
Nick
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Default Pindel memory usage 30x whole genome

How much memory should Pindel be using on a 30x whole genome? With the smallest window size it is using a large amount of memory even when the log says it is processing a window with only 1000 reads.
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Old 02-12-2015, 06:28 AM   #2
KaiYe
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can you tell me your Pindel version? You could split calculation by 5MB per job. Sometimes there is extreme high coverage at a few small regions. This causes maximum memory usage going high.

Kai
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Old 02-12-2015, 06:36 AM   #3
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The version was 0.2.5a4, May 2 2014. We tried using the smallest window (.01) but still maxed out 30Gb of memory.
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Old 02-12-2015, 06:40 AM   #4
KaiYe
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Quote:
Originally Posted by Nick View Post
The version was 0.2.5a4, May 2 2014. We tried using the smallest window (.01) but still maxed out 30Gb of memory.
Is it possible to send me the log file or console output to my email kye@genome.wustl.edu?
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