UnitigResolver MBG Issue

[nickgladman]

Hello. Thanks so much for providing this resource to the community! I'm doing a test run on some HiFi reads and discovered this in the buildGraph.err log:

MBG: src/UnitigResolver.cpp:707: std::pair<UnitigGraph, std::vector<ReadPath> > resolvableToUnitigs(const ResolvableUnitigGraph&, const std::vector<PathGroup>&, const std::vector<ReadPathInfo>&): Assertion `coverages[i][j] > 0' failed.
./buildGraph.sh: line 41: 3559810 Aborted                 (core dumped) /grid/ware/home/gladman/software/verkko/bin/MBG $iopt -t 4 -k 1001 -r 15000 -R 4000 -w 100 --kmer-abundance 1 --unitig-abundance 2 --error-masking=collapse-msat --output-sequence-paths ../1-buildGraph/paths.gaf --hpc-variant-onecopy-coverage 25 --do-unsafe-guesswork-resolutions --out ../1-buildGraph/hifi-resolved.gfa

Not sure if this is like issue #67 or if something else needs to be done. I was directed the the buildGraph.err logs after checking the snakemake log--there was a Error in rule buildGraph: flag in the file.

verkko output file:

Launching bioconda verkko bioconda 1.2
Using snakemake 7.22.0.

[skoren]

Since your verkko and presumably MBG aren't the latest releases, I'd first try updating both to see if the error is resolved. You should be able to resume the old assembly with the new version once it's installed from conda.

[nickgladman]

Thanks. I thought I installed the newest version from Conda, but I was mistaken. Silly mistake.

[nickgladman]

Hello. I re-installed and re-ran but still ended up with the identical error.

Here are my versions for MBG and GraphAligner:

$ MBG --version
MBG bioconda 1.0.14
Version: bioconda 1.0.14

$ GraphAligner --version
GraphAligner bioconda 1.0.17-
GraphAligner bioconda 1.0.17-
Version bioconda 1.0.17-

$ output file:
Launching bioconda verkko bioconda 1.3.1
Using snakemake 7.24.0.

[skoren]

Can you share the hifi-corrected.fasta.gz file, see https://canu.readthedocs.io/en/latest/faq.html#how-can-i-send-data-to-you

[nickgladman]

Hello. Sorry for the delay. I have been trying to upload the files as instructed, but I am getting an error with my ftp permissions. As soon as I resolve that I'll let you know it's been pushed to the incoming/sergek directory.

[nickgladman]

Hello again. We resolved the ftp issue. The corrected reads should be in the incoming/sergek folder, labeled as ng_hifi-corrected.fasta.gz.

[nickgladman]

Hello. I'm just checking to make sure that my corrected fasta files were successfully uploaded. Thanks.

[skoren]

Yes, sorry for the silence, this dropped of my radar. I'm testing the latest MBG now since there have been some fixes since this time and will see if it still crashes and update this issue.

[skoren]

@maickrau this still seems to be crashing in the latest MBG, could you take a look. The reads are in the globus share under issue130.

[maickrau]

The most recent MBG commit should fix this

[nickgladman]

@maickrau would this be release 17 of MBG? Version 1.0.14 from February 2023?

[maickrau]

The most recent MBG commit, for example b468b37. It's not in a release yet so you have to compile it from source or wait for the next release.

[skoren]

I presume this is resolved? Re-open if not.