genotype error

[RaSieb]

Hey,
I am trying to set up genotype with your example data, but keep on getting this error:

[14 May 2016 00:48:13-MUD][memory] We made 20 allocs
[14 May 2016 00:48:13-MUD] Done.
[14 May 2016 00:48:13-MUD][time] 14.00 seconds
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/2.7/bin/mykrobe", line 9, in
load_entry_point('mykrobe==0.3.3', 'console_scripts', 'mykrobe')()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 98, in main
args.func(parser, args)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mykrobe/mykrobe_predictor.py", line 31, in run_subtool
run(parser, args)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mykatlas/cmds/genotype.py", line 51, in run
print(json.dumps(run_main(parser, args), indent=4))
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/mykatlas/cmds/genotype.py", line 42, in run_main
variant_confidence_threshold=args.min_variant_conf,
AttributeError: 'Namespace' object has no attribute 'min_variant_conf'

My input string is:
mykrobe genotype asada example-data/staph-amr-bradley_2015.fasta -1 /seqs/a_S30_L001_R1_001.fastq.gz /seqs/a_S30_L001_R2_001.fastq.gz

The sequences run fine in predict with the latest version installed.

Thanks in advance for any advise!

[Phelimb]

Thanks!

This was caused by an update in the API of an underlying library. This should be fixed in 9d196c7.

To update run:

pip install mykrobe --upgrade

[Phelimb]

mykrobe --version

should return

mykrobe v0.3.6*

[RaSieb]

Yeps, thanks a lot!
It works perfectly now.