Alternative alignment algorithms fail assertion

[kevinxchan]

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]

I am also receiving this error using sggotoh

[jwasmuth]

As am I