Error in rule buildGraph:

[sigau]

Hello. Thanks so much for providing this resource to the community!
I instal verkko using conda.
I was trying to co-assemble hifi and ont data using verkko and encounter the following error :

"
Error in rule buildGraph:
jobid: 4
input: hifi-corrected.fasta.gz
output: 1-buildGraph/hifi-resolved.gfa, 1-buildGraph/hifi_nodecov.csv, 1-buildGraph/paths.gaf
log: 1-buildGraph/buildGraph.err (check log file(s) for error details)
shell:
"
And when I look at the log file I have this :

MBG: src/HPCConsensus.cpp:145: std::vector<std::tuple<long unsigned int, long unsigned int, long unsigned int, long unsigned int, bool, long unsigned int, long unsigned int> > getMatchBlocks(const std::vector<std::vector >&, const UnitigGraph&, const ReadPath&, std::vector, size_t, size_t): Assertion `readEnd - readStart == unitigEnd - unitigStart' failed.
Aborted

I saw in the issue #67 that it could be the version of MBG (1.0.10) but mine is more recent (1.0.14).

buildGraph.err.txt
verkko_assembly.e.txt
verkko_assembly.out.txt

[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

[sigau]

Sure :
https://filesender.renater.fr/?s=download&token=ace316b8-865c-43b0-b542-e5f0c7f1b905

[maickrau]

Newest MBG commit 20d493d should now fix this.

[sigau]

Hi,
I retry to run verkko with the last commit of MBG but still get the same error with the rule buildGraph

[maickrau]

That's strange, my manual run worked. Could you check that 1-buildGraph/buildGraph.err has this version info somewhere near the start: MBG Branch master commit 20d493dcac1f812428b0efab4914b44dbea2629a

[sigau]

buildGraph.err.txt
it seems to be the right release

[maickrau]

Yes, it's the right version. Looks like this hit some nondeterminism bug in MBG. The error is same as MBG issue 19 maickrau/MBG#19 but your run and my run have slightly different results based on logs, and this difference was enough to cause a crash.

[sigau]

Ok so should wait for the next update of MBG ?

[maickrau]

You can try rerunning and hope that the nondeterminism just happens to not crash, or wait for an update.

[maickrau]

Now you can try rerunning with the latest MBG version which fixed the error in the other issue. My rerun did not run into this issue due to nondeterminism so I couldn't verify if it fixed this issue, but if it was caused by the same bug then it should run.

[sigau]

Hi !
Effectively this resolve my problem with this error for the rule buildGraph but got an new error with the rule processONT now should I open a new issue ?

[skoren]

Yes, open a new issue for that.