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GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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Issue when using --no-end2end #78

Open awjga opened 6 years ago

awjga commented 6 years ago

Hi,

I am running into some issue when trying to use the --no-end2end option. This is the code that I had use: graphmap align -a anchorgotoh --no-end2end -r cp_nanopore.fa -d try.fasta -o unmod.noend2end.sam

Resulted in this error: [CPU time: 32.60 sec, RSS: 278 MB] Read: 8062/437624 (1.84%) [m: 684, u: 7359], length = 402, qname: 4a442670-c846-474b-8d64-c4f298b613d...graphmap: src/alignment/cigargen.cc:607: std::string AlignmentToMD(std::vector&, const int8_t*, int64_t): Assertion `alignment_position_start >= 0 && "Serious problem with MD calculation, stemmed from alignment somewhere."' failed

I had also tried: graphmap align -a anchor --no-end2end -r cp_nanopore.fa -d try.fasta -o unmod.noend2end.sam

Also resulted in a similar error: [CPU time: 46.95 sec, RSS: 278 MB] Read: 8073/437624 (1.84%) [m: 686, u: 7368], length = 169, qname: fd234602-1710-478f-8c85-d8d6150319b...graphmap: src/alignment/cigargen.cc:607: std::string AlignmentToMD(std::vector&, const int8_t*, int64_t): Assertion `alignment_position_start >= 0 && "Serious problem with MD calculation, stemmed from alignment somewhere."' failed. Aborted (core dumped)

mariuswalter commented 5 years ago

I have the same problem, if you found to a solution..