iqbal-lab/Mykrobe-predictor

mykrobe predict: error: argument species:

Closed this issue · 3 comments

hirenbioinfo commented

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

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

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

hirenbioinfo commented

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'