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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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Alternative alignment algorithms fail assertion #100

Open kevinxchan opened 5 years ago

kevinxchan commented 5 years ago

I'm currently trying to align some nanopore datasets to a reference composed of recA sequences from different prokaryotes. The default anchor algorithm works fine for all datasets I'm using, but when I try to use sg and sggotoh they all fail on some datasets due to an assertion failure. What do you think could be the problem? Here's the error message, and an example log output is attached below.

graphmap: src/alignment/cigargen.cc:525: int CountAlignmentOperations(std::vector<unsigned char>&, const int8_t*, const int8_t*, int64_t, int64_t, SeqOrientation, int64_t, int64_t, int64_t, int64_t, bool, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*): Assertion `alignment_position_start >= 0 && "Serious problem in counting alignment operations, stemmed from alignment somewhere."' failed.
/home/kchan/scripts_thesis/shell/run_graphmap.sh: line 85:  8678 Aborted                 $GRAPHMAP align --alg sg --threads $THREADS -r $reference --index $index_file --extcigar --reads $WORK_DIR/raw_data/$name.fastq.gz -o $WORK_DIR/processed/graphmap/$name/sg_eval1e-5.sam

log_single.log

cchrysostomou commented 5 years ago

I am also receiving this error using sggotoh

jwasmuth commented 5 years ago

As am I