search

iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
Other
50 stars 19 forks source link

confidence_threshold bug #143

Closed Takadonet closed 5 years ago

Takadonet commented 6 years ago

Was getting the following stacktrace when running the latest version of mykrobe on bioconda. (0.5.6)

Example command : mykrobe predict tb_sample tb -1 ERR117639_1.fastq.gz

Traceback (most recent call last): File "/share/apps/conda_env/mykrobe-v0.5.6.0/bin/mykrobe", line 6, in <module> sys.exit(mykrobe.mykrobe_predictor.main()) File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykrobe/mykrobe_predictor.py", line 125, in main args.func(parser, args) File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykrobe/mykrobe_predictor.py", line 34, in run_subtool run(parser, args) File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykrobe/cmds/amr.py", line 192, in run gt.run() File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykatlas/typing/typer/genotyper.py", line 300, in run self._type() File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykatlas/typing/typer/genotyper.py", line 304, in _type self._type_variants() File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykatlas/typing/typer/genotyper.py", line 338, in _type_variants call = gt.type(probe_coverages, variant=probe_name) File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykatlas/typing/typer/variant.py", line 77, in type variant_probe_coverage, variant)) File "/share/apps/conda_env/mykrobe-v0.5.6.0/lib/python3.5/site-packages/mykatlas/typing/typer/variant.py", line 119, in _type_variant_probe_coverages if "LOW_GT_CONF" in self.filters and (confidence < self.confidence_threshold): TypeError: unorderable types: int() < NoneType()

It will not work with any of my test datasets and is only resolved by passing a value to --min-variant_conf . Temporary workaround example would be mykrobe predict tb_sample tb -1 ERR117639_1.fastq.gz --min_variant_conf 0

iqbal-lab commented 6 years ago

I'm sorry this issue has been ignored. We're about to move mykrobe to a new codebase and repo. When that is live, I'll return, close this issue and point you at the new code.

Phelimb commented 5 years ago

@Takadonet This may be fixed in https://github.com/Mykrobe-tools/mykrobe