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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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mykrobe errors with: AttributeError: 'Namespace' object has no attribute 'ont' #120

Closed antunderwood closed 5 years ago

antunderwood commented 7 years ago

Running Python 2.7.11 I get the following error

INFO:root:Running AMR prediction with panels data/panels/tb-species-160330.fasta.gz, data/panels/tb-amr-walker_2015.fasta.gz
INFO:root:Running AMR prediction with panels data/panels/tb-species-160330.fasta.gz, data/panels/tb-amr-walker_2015.fasta.gz
Traceback (most recent call last):
  File "../mykrobe/bin/mykrobe", line 9, in <module>
    load_entry_point('mykrobe==0.4.3', 'console_scripts', 'mykrobe')()
  File "/home/local/GEL/anthony/software/mykrobe/lib/python2.7/site-packages/mykrobe-0.4.3-py2.7.egg/mykrobe/mykrobe_predictor.py", line 130, in main
    args.func(parser, args)
  File "/home/local/GEL/anthony/software/mykrobe/lib/python2.7/site-packages/mykrobe-0.4.3-py2.7.egg/mykrobe/mykrobe_predictor.py", line 34, in run_subtool
    run(parser, args)
  File "/home/local/GEL/anthony/software/mykrobe/lib/python2.7/site-packages/mykrobe-0.4.3-py2.7.egg/mykrobe/cmds/amr.py", line 117, in run
    if args.ont:
AttributeError: 'Namespace' object has no attribute 'ont'
Phelimb commented 7 years ago

Thanks @aunderwo .

Could you paste the output of pip freeze in here? Looks like the version of mykatlas (a dependancy) could be incompatible with this version of mykrobe.

antunderwood commented 7 years ago

Hi @Phelimb I think this can be closed. I was trying to install using python setup.py install --prefix=... in order to install to a non standard location. I can install with pip install and virtualenv so will now try with my newly discovered command of pip install -t