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shingocat / lrscaf

TGS scaffolding
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LRScaf-1.1.8 stuck at "Finding repeats" #14

Closed bvaldebenitom closed 4 years ago

bvaldebenitom commented 4 years ago

Hi!

I've been running LRScaf, and since yesterday it apparentely hasn't done anything. The last line of the log is: 2020-01-04 17:27:40 [ INFO ] Finding repeat, erase time: 1948 ms When using "top" the process appears with state S (interruptible sleep (waiting for an event to complete), https://idea.popcount.org/2012-12-11-linux-process-states/)

Any clue regarding this? How long should I expect this step to last?

The minimap alignment file is a 4.1 Gb file, the contigs file is a 4.3 Gb file, and current memory usage of LRScaf seem to be ~16 Gb.

shingocat commented 4 years ago

Hi bvaldebenitom,

The next step is to build links from alignment after the finding repeat step. As you stated, the alignment records are much large. It will take time to do that. You could try to use multi-threads to speed up this process.

xiekunwhy commented 4 years ago

LRScaf-1.1.9 stuck at "Finding repeats" too.

shingocat commented 4 years ago

hi xiekunwhy,

You could try to use multi-threads options or fliter the small contigs by minContiglenght option.