out of memory

[Former user]

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

[Vlado Boza]

Hello Luigi, do you know how big is your largest read? Or can you please, send us ([e-mail]) 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).

[Luigi Faino]

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

[ragak]

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?

[Vlado Boza]

I added option for filtering out long reads.

[ragak]

Awesome thanks