mothur

Error when using multiple cutoffs

Hi,

when running the following:

cluster.split(column=current, count=current, taxonomy=current, cutoff=0.10-0.05-0.03, taxlevel=6, splitmethod=classify, method=opti)

I get this error:

[ERROR]: 0.10-0.05-0.03RAM used: 11.1359Gigabytes . Total Ram: 125.652Gigabytes.

has occurred in the Utils class function mothurConvert-double. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry

Can you use only cutoff=0.03 and let us know what happens?

FWIW, people generally try cutoffs like 0.05 and 0.10 because they’re trying to approximate the genus and family levels. If that’s what you want, you’d be better served by using the phylotype function to get data at those levels.

Pat

with cutoff=0.03 it works fine. I worked with 0.05-0.03 but not with more than two cutoffs.

The problem is that with a larger cutoff you save more distances and are sucking up all of your computer’s RAM. You could get a computer with more RAM (e.g. high memory node on your institution’s cluster or use AWS) or be more aggressive with the number of diffs in pre.cluster.

Is there a reason you need 0.05 or 0.10?

Pat

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