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Old 01-18-2012, 06:29 AM   #1
jfellows88
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Default BFAST Alignment Troubleshoot

Hi

I am trying to perform an alignment in colored space with SOLID and I get this error


In function "RGMatchesRead": Fatal Error[MallocMemory]. Variable/Value: m->ends.
Message: Could not allocate memory.
***** Exiting due to errors *****


Here is the code I used

/usr/local/bfast/0.6.5a/bin/bfast localalign -f c_elegans.WS214.dna.fa -A 1 -m c_elegans.WS214.dna.fa.cs.1.1.bif


Does anyone have any thoughts or helpful tips? Thanks
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Old 01-18-2012, 10:13 PM   #2
arvid
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That looks like it cannot allocate enough memory - how much RAM do you have on your machine?
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Old 01-23-2012, 07:04 AM   #3
jfellows88
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3 GB.

This should be sufficient, right?
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Old 01-24-2012, 12:23 AM   #4
arvid
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Not necessarily, it seems that BFAST it quite RAM hungry, needing about 17-24 GB RAM for an index of the human genome (according to the paper).
You might want to try bowtie or some other low-mem aligner...
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