out of memory
Issue #1
new
Dear Developers, i have an issue running Deepnano. when I run the consensus call without Metricor, I run out of memory in the align2d step. i have 256 Gb of ram on this machine.
could you help, please?
thanks Luigi
Comments (5)
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repo owner -
well, it would be nice to know which file makes the error. however, i can not find it. can you suggest how to find it?
Luigi
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Hi, I have a similar problem while running the basecall without metrichor. The program slows down the entire server. In the data set I am using, there are a couple of really long reads (that metrichor calls as 'failed') - would it help to filter those out beforehand?
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repo owner I added option for filtering out long reads.
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Awesome thanks
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Hello Luigi, do you know how big is your largest read? Or can you please, send us (bozavlado@gmail.com) the file, which crashes your basecalling?
(currently the align2d is written in very lazy way with time complexity O(n^2), we will try to rewrite this soon).