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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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mykrobe predict: error: argument species: #122

Closed hirenbioinfo closed 5 years ago

hirenbioinfo commented 7 years ago

mykrobe predict ERR117639 ./ERR117639*.gz tb

Error : mykrobe predict: error: argument species: invalid choice: 'demo_input_file_for_M.tuberculosis_app.fastq' (choose from 'staph', 'tb')

iqbal-lab commented 7 years ago

Your arguments are in the wrong order. Check the Readme. Should be

Mykrobe predict ERR117639 tb -1 ./ERR...gz

hirenbioinfo commented 7 years ago

Could not make it out. Can you please have a look $mykrobe predict ERR117639 tb -1 ./ERR117639*.gz
Last few lines of error message WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-C517T WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-C517G WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-G1484A WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-G1484T WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-G1484C WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-G515A WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-G515T WARNING:mykatlas.typing.typer.genotyper:Fewer ref alleles than alt alleles for alt-G515C Traceback (most recent call last): File "/home/user1/bin/mykrobe", line 11, in sys.exit(main()) File "/home/user1/.local/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 99, in main args.func(parser, args) File "/home/user1/.local/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 32, in run_subtool run(parser, args) File "/home/user1/.local/lib/python2.7/site-packages/mykrobe/cmds/amr.py", line 180, in run sequence_confidence_threshold=args.min_gene_conf
TypeError: init() got an unexpected keyword argument 'include_hom_alt_calls'

Phelimb commented 5 years ago

@hirenbioinfo this should be fixed in https://github.com/Mykrobe-tools/mykrobe