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Old 11-16-2012, 06:26 AM   #1
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Location: Tübingen

Join Date: Jan 2012
Posts: 9
Default bowtie chunkmbs - Exhausted best-first chunk memory


perhaps somebody can solve this little mystery for me.

Running bowtie --chunkmbs 512 worked without any errors/warnings.
As the mapping statistic was not as I expected, among other things, I also increased the value for chunkmbs to 4096. However, on the same dataset, with the other parameters untouched, bowtie now reports "Exhausted best-first chunk memory for read..." millions of times.
At this point, the sever was using only 10% of it's overall memory.

Could somebody explain this to me please?
ChrisAU is offline   Reply With Quote
Old 02-17-2014, 12:53 PM   #2
Location: New York

Join Date: Dec 2010
Posts: 40

Hi ChrisAU,

Did you solve your problem? I am now having the same issue and I could use a little bit of help.

alisrpp is offline   Reply With Quote

bowtie, chunkmbs, memory

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