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marbl / verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
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Error of 4-processONT #268

Closed YouxinZhao closed 3 months ago

YouxinZhao commented 4 months ago

I am using R10 ONT data corrected with dorado（SUP）herro model to assemble the genome. Two jobs all stopped for error of 4-processONT.

ont_resolved_graph.gfa.err image

YouxinZhao commented 4 months ago

Verkko V2.1

YouxinZhao commented 4 months ago

ont_resolved_graph.gfa.err: https://github.com/marbl/verkko/assets/95477328/abe7e101-ebab-4f2f-a419-4d6a531af523

maickrau commented 4 months ago

Could you share the following files:

4-processONT/normal-connected.gfa
4-processONT/fake-ont-nodecovs.csv
4-processONT/fake-ont-alns.gaf
YouxinZhao commented 4 months ago

The files were uploaded. https://figshare.com/articles/dataset/Verkko_error/26308852

maickrau commented 4 months ago

Commit 7248729 in master branch should fix this bug

skoren commented 3 months ago

I presume this is fixed? It should be part of the next release which should be available in the next couple of weeks.