bowtie chunkmbs - Exhausted best-first chunk memory

ChrisAU · 11-16-2012, 06:26 AM

Hi,

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?
Chris

alisrpp · 02-17-2014, 12:53 PM

Hi ChrisAU,

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

Thanks!

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11-16-2012, 06:26 AM	#1
ChrisAU Junior Member Location: Tübingen Join Date: Jan 2012 Posts: 9	bowtie chunkmbs - Exhausted best-first chunk memory Hi, 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? Chris

02-17-2014, 12:53 PM	#2
alisrpp Member 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. Thanks!