Error from UnitigResolver addPathButFirstMaybeTrim

[slmcevoy]

Hi,

I'm trying to run Verkko on some plant HiFi and ONT and get the error pasted below. I would greatly appreciate any help figuring out how to move forward. Thanks!

MBG Branch master commit f9303c51cdbaed401d199d18290638c4b37f61c5 2023-01-17 13:53:23 +0200 Parameters: k=1001,w=100,a=1,u=2,t=4,r=15000,R=4000,hpcvariantcov=25,errormasking=collapse-msat,endkmers=no,blunt=no,keepgaps=no,guesswork=yes,copycountfilter=no,onlylocal=no,cache=no Collecting hpc variant k-mers Reading sequences from ../hifi-corrected.fasta.gz 513709214 total selected k-mers in reads 137912719 distinct selected k-mers in reads Reading sequences from ../hifi-corrected.fasta.gz Collecting selected k-mers Reading sequences from ../hifi-corrected.fasta.gz 513709214 total selected k-mers in reads 137914062 distinct selected k-mers in reads Unitigifying Filtering by unitig coverage 4684564 distinct selected k-mers in unitigs after filtering Getting read paths Reading sequences from ../hifi-corrected.fasta.gz Resolving unitigs 1086386 unitigs before resolving estimated average coverage 8.72569 6354302 raw read paths 6394203 raw read paths 2694860 read paths removed 26387 tips removed 54 crosslinks removed 4045 nodes and 1 edges try resolve k=1001unresolvable even length exact palindrome frozen, id: 492957 unresolvable even length exact palindrome frozen, id: 725696 unresolvable even length exact palindrome frozen, id: 118815 , replaced 28232 nodes with 109561 nodes, unitigified 182177 nodes to 67178 nodes removed 4201 nodes and 161 edges MBG: src/UnitigResolver.cpp:954: void addPathButFirstMaybeTrim(ResolvableUnitigGraph&, std::vector&, PathGroup&&): Assertion `newPath.path.size() > 0' failed. ./buildGraph.sh: line 41: 58078 Aborted /public/groups/meyerlab/software/MBG/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

[maickrau]

This should be fixed in b706a44, could you try with that and then close if it works

[slmcevoy]

Thanks for the update. It went a little farther and threw a different error:

... 268334 unitigs after resolving Building unitig sequences Reading sequences from ../hifi-corrected.fasta.gz MBG: src/ConsensusMaker.cpp:238: std::pair<std::vector, StringIndex> ConsensusMaker::getSequences(): Assertion `maxCount > 0' failed. ./buildGraph.sh: line 41: 8848 Aborted /public/groups/meyerlab/software/MBG/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

[maickrau]

Could you please share hifi-corrected.fasta.gz?

[slmcevoy]

I have temporarily made the file available here: http://public.gi.ucsc.edu/~sumcevoy/ Thanks for looking into it!

[slmcevoy]

Hi Mikko, Were you able to access the file ok? I would like to remove it from that location if so.

[maickrau]

Yes, I was able to download them and you can remove them.

[maickrau]

This should now work with commit 1611e9f

[slmcevoy]

It successfully ran without any issues. Thanks so much for the fix!