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Old 05-29-2009, 03:10 PM   #1
tgenahmet
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Default BWA memory issues

We're trying to use BWA with paired end reads (bwa sampe with default settings) and running into memory problems when aligning to whole human genome. It maxes out our memory on a machine with 24GB of RAM even with 12K reads.

Anyone else having similar issues?
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Old 06-03-2009, 12:56 AM   #2
lh3
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What is the length of your reads?
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Old 06-03-2009, 01:09 PM   #3
tgenahmet
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We were running it with 36bp reads.
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Old 06-04-2009, 02:55 AM   #4
lh3
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I have only tested bwa for SOLiD data on one run and it works fine. I am not sure why it costs so much memory for your data. What is peak memory usage? Could that be because your machine has other processes using a lot of memory?
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