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Old 05-07-2014, 12:57 AM   #37
Senior Member
Location: Germany

Join Date: Apr 2012
Posts: 215

Dear Brian,

I tested bbmap successfully on a small dataset and so far I'm very happy with the results
However, I'm running into some memory problems using my real dataset:

My RAM looks currently as follows:
total used free shared buffers cached
Mem: 66066316 42861240 23205076 0 3700 42478768
When I now run bbmap with different -Xmx setting or also without the parameter, it always quits with:

Max Memory = 28633 MB (or other, depending on the value I used)
Available Memory = 10830 MB (ranging from 8Gb - 12Gb)
Reducing threads from 16 to 15 due to low system memory.
java.lang.RuntimeException: java.lang.OutOfMemoryError: Java heap space
To me it looks like a bug within the memory detection or am I missing something?
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