--ont flag gives error message

Hi, I encounter python ValueError when running the program with flag --ont but it works well without --ont.

The version I am using is v0.5.6-0-gbd7923a-dirty (installed via conda, Python 2.7.15) The command used is:

python ~/tools/Mykrobe-predictor/mykrobe/mykrobe_predictor.py predict sample tb -1 sample.fasta --mccortex31_path ~/tools/Mykrobe-predictor/mccortex/bin/mccortex31 --ont

The error message is:

Traceback (most recent call last):
  File "/data/chengyee/tools/Mykrobe-predictor/mykrobe/mykrobe_predictor.py", line 135, in <module>
    main()
  File "/data/chengyee/tools/Mykrobe-predictor/mykrobe/mykrobe_predictor.py", line 126, in main
    args.func(parser, args)
  File "/data/chengyee/tools/Mykrobe-predictor/mykrobe/mykrobe_predictor.py", line 35, in run_subtool
    run(parser, args)
  File "/data/chengyee/anaconda2/lib/python2.7/site-packages/mykrobe/cmds/amr.py", line 192, in run
    gt.run()
  File "/data/chengyee/anaconda2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 300, in run
    self._type()
  File "/data/chengyee/anaconda2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 304, in _type
    self._type_variants()
  File "/data/chengyee/anaconda2/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 338, in _type_variants
    call = gt.type(probe_coverages, variant=probe_name)
  File "/data/chengyee/anaconda2/lib/python2.7/site-packages/mykatlas/typing/typer/variant.py", line 77, in type
    variant_probe_coverage, variant))
  File "/data/chengyee/anaconda2/lib/python2.7/site-packages/mykatlas/typing/typer/variant.py", line 125, in _type_variant_probe_coverages
    int(i) for i in gt.split("/")],
ValueError: invalid literal for int() with base 10: '-'

Please advice. Thanks, Cheng

iqbal-lab / Mykrobe-predictor

--ont flag gives error message #151