src/hmm/nanopolish_profile_hmm_r9.cpp:81: std::vector<HMMAlignmentState> profile_hmm_align_r9(const HMMInputSequence&, const HMMInputData&, uint32_t): Assertion `n_events >= 2' failed.

[macieksk]

nanopolish: src/hmm/nanopolish_profile_hmm_r9.cpp:81: std::vector profile_hmm_align_r9(const HMMInputSequence&, const HMMInputData&, uint32_t): Assertion `n_events >= 2' failed.

/bin/bash: line 1: 41635 Aborted nanopolish variants -w hg38_ct_UserTrack:50000-60700 -r /dev/shm/nanopolish/reads.fasta -b align.bam -g refseq.fa -t 8 -v -v -v --ploidy 2 --calculate-all-support --min-candidate-frequency 0.2 --max-haplotypes=4096 --min-candidate-depth=20

Hi, I'm getting the above error in one subrange of my variant calling region. What does it indicate? Can I walk around it somehow, since this prevents output of variants from the whole subregion. I tried changing the above assert to assert(n_events >= 1); but then I got

nanopolish: src/hmm/nanopolish_profile_hmm_r9.cpp:125: std::vector profile_hmm_align_r9(const HMMInputSequence&, const HMMInputData&, uint32_t): Assertion `get(vm, row, col) != -(__builtin_inff())' failed.

So I commented out this assertion too, and it seems to have worked. It affects the value of as.l_fm = get(vm, row, col); though as.l_fm seems to be used only in print_debug_stats. Is it safe to run this code?

[jts]

It probably isn't safe to run the code after commenting out these assertions - there is a good chance it will output erroneous variants in this case. Could you provide your reads that trigger this assertion so I can reproduce the problem?