--ont flag gives error message
Closed this issue · 1 comments
cytang19 commented
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
Phelimb commented
@cytang19 could you reinstall with the latest version from https://github.com/Mykrobe-tools/mykrobe and see if this resolves your issue?