Assertion issue

[asylvz]

Hi,

I'm trying to align an assembly to minigraph cactus using the command below. However I get the following error:

GraphAligner -g hprc-v1.1-mc-chm13.gfa -f XXX.fasta.gz -a {output} -t 24 -- bandwidth 30 --multimap-score-fraction 0.99 
--precise-clipping 0.9 --min-alignment-score 2000 --seeds-mem-count 100000 --seeds-mxm-windowsize 10000 
--seeds-mxm-cache-prefix {output_path}/ga_prefix

However, this is the error I get:

src/GraphAlignerBitvectorBanded.h:536: Assertion 'currentSlice.node(i).minScore <= 
currentSlice.node(i).startSlice.scoreEnd' failed. Read: haplotype1-0000027. Seed: 0+,0,0,0

[maickrau]

Hi, could you upload the graph and the read?

[asylvz]

With lower bandwidth it got resolved but I cannot regenerate this issue currently. I will let you know if I see this again but now I have a similar issue with a different sample:

GraphAligner -g hprc-v1.1-mc-chm13.gfa -f HG02953.vrk-ps-sseq.asm-hap2.fasta.gz -a HG02953_hap2.gaf -t 16 -- 
bandwidth 15 --multimap-score-fraction 0.99 --precise-clipping 0.9 --min-alignment-score 2000 --seeds-mem-count 
100000 --seeds-mxm-windowsize 10000 --seeds-mxm-cache-prefix snake_alignments/ga_prefix

And the error:

src/GraphAligner.h:647: Assertion 'trace.trace[i].DPposition.seqPos == trace.trace[i-1].DPposition.seqPos || 
trace.trace[i].DPposition.seqPos == trace.trace[i-1].DPposition.seqPos+1' failed. Read: haplotype2-0000154. Seed: 
0+,0,0,0

Reads: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/working/20230818_verkko_batch1/assemblies/HG02953/HG02953.vrk-ps-sseq.asm-hap2.fasta.gz

Graph: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-chm13/hprc-v1.1-mc-chm13.gfa.gz

[yuand2022]

Yes, I also found a lot of assertions, I don’t know how to deal with it. I am using GraphAlinger v1.0.19 version