MBG: Assertion `resolvableGraph.unitigLength(newUnitigs[i].first[0].first) < resolvableGraph.unitigLength(newUnitigs[i].second)' failed

[oushujun]

Hello,

I am using verkko bioconda 1.0 and run it locally. I run it with all default parameters:
verkko -d asm0428 --hifi Tanz-1.q20.fastq.gz --nano Nanopore_Tanz_all_reads_Guppy6_Sup_model.fq --threads 48

Errors in 1-buildGraph/buildGraph.err

try resolve k=1319, replaced 21 nodes with 161 nodes, unitigified 271 nodes to 133 nodes
try resolve k=1320, replaced 24 nodes with 199 nodesMBG: src/UnitigResolver.cpp:765: void replacePathNodes(ResolvableUnitigGraph&, std::vector&, const std::vector<std::pair<std::vector<std::pair<long unsigned int, bool> >, long unsigned int> >&): Assertion `resolvableGraph.unitigLength(newUnitigs[i].first[0].first) < resolvableGraph.unitigLength(newUnitigs[i].second)' failed.
./buildGraph.sh: line 39: 67899 Aborted (core dumped) /home/sou6/bin/MBG/bin/MBG $iopt -t 8 -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 --out ../1-buildGraph/hifi-resolved.gfa

Is it due to the MBG version included in the conda recipe?

Thanks,
Shujun

[skoren]

It may be a bug in the latest MBG version. Can you confirm the versions of verkko/mbg/graphaligner you're running by running them with --version?

[oushujun]

$ verkko --version
bioconda verkko bioconda 1.0

$ MBG --version
MBG Branch master commit de2b7e859e9710259f199830ec6a18643d1435ae 2022-04-27 12:02:30 +0200
Version: Branch master commit de2b7e859e9710259f199830ec6a18643d1435ae 2022-04-27 12:02:30 +0200

$ GraphAligner --version
GraphAligner Branch master commit 6bd37e23a300b1ca684891fc39ebfe0072286b9c 2022-04-19 21:23:17 +0200
GraphAligner Branch master commit 6bd37e23a300b1ca684891fc39ebfe0072286b9c 2022-04-19 21:23:17 +0200
Version Branch master commit 6bd37e23a300b1ca684891fc39ebfe0072286b9c 2022-04-19 21:23:17 +0200

[maickrau]

This is a bug in the current MBG master version. You can try running with MBG version 1.0.10

[skoren]

Yes, I was going to say, neither MBG nor GraphAligner look like they're installed from Conda, those should report versions like:

% GraphAligner --version
GraphAligner bioconda 1.0.16
GraphAligner bioconda 1.0.16
Version bioconda 1.0.16

% MBG --version
MBG bioconda 1.0.10
Version: bioconda 1.0.10

By default, verkko will use MBG/GraphAligner in your path or in <path to verkko binaries/..//lib/verkko/bin if it's not in path. However, you can explicitly control which MBG/GraphAligner is used by verkko using the --mbg and --graphaligner options

[oushujun]

I see. It may picked up the old versions. Let me reinstall and retry. Thanks!

[oushujun]

Issue resolved. Thanks!