src/UnitigResolver.cpp:716 Assertion `coverages[i][j] > 0' failed

[dehui333]

Hi,

I was running verkko on some ULONT reads corrected by herro (https://github.com/lbcb-sci/herro). Although they are quite different from hifi reads but most runs using verkko and hifiasm have been successful. There is however one run which crashed with the following error in buildGraph.err:

MBG: src/UnitigResolver.cpp:716: std::pair<MBG::UnitigGraph, std::vector<MBG::ReadPath> > MBG::resolvableToUnitigs(const MBG::ResolvableUnitigGraph&, const std::vector<MBG::PathGroup>&, const std::vector<MBG::ReadPathInfo>&): Assertion `coverages[i][j] > 0' failed.

I was running it with default settings so the reads were further corrected by Canu - I have uploaded the reads (dehui_fix2_hifi-corrected.fasta.gz) to incoming/sergek. The log file is at dehui_buildGraph.err.

Please delete dehui_hifi-corrected.fasta.gz and dehui_fix_hifi-corrected.fasta.gz as those are terminated partial uploads due to slowness from where I was trying to upload them from. Sorry for that!

More information: Was initially running verkko commit 9ee717e97d2460c4d960ad45827e83ac888bf04f (march 19 2024) with MBG Branch HEAD commit c4af4fc7e13a1ad3f8b5c5dc333cf2ac8d0d6946 2024-01-22 15:04:51 +0200 - which crashed with the mentioned error.

Updated verkko to b050ef42e33ce0ac5bd806746172ae15c4c2dcae 2024-03-25 18:13:14 -0400 and MBG to 10782bdeb38e6cd33918479e3f13413173aeb284 2024-03-11 13:13:15 +0200 - resumed the run from where it stopped, crashed again with the same error.

Please let me know if you need any other information. Thank you!