Can't run adVNTR genotype - unexpected keyword argument 'max_prob'

[hevmarriott]

Hi there,

I have been trying to run adVNTR (latest version) via conda and every time it gives me this error:

Traceback (most recent call last):

File "/users/k19042397/miniconda2/envs/adVNTR/bin/advntr", line 11, in <modu$ sys.exit(main()) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/ad$ genotype(args, genotype_parser) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/ad$ genome_analyzier.find_repeat_counts_from_alignment_file(input_file, averag$ File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/ad$ average_coverage, update) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/ad$ retval = func(*args, **kwargs) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/ad$ max_prob=0) # No probability for the estimated genotype TypeError: init() got an unexpected keyword argument 'max_prob'

I do not know whether this is a disagreement between init GenotypeResult, which does not have max_prob assigned and defined further down, only max_likelihood, or if it is a problem with my options. I assigned a float to the coverage option and played around with the options and it still gives me this.

Any help would be much appreciated.

All the best,

Heather

[hevmarriott]

Hi Sorry, it seems it cut off most of the code

Here is the updated version:

Traceback (most recent call last):

File "/users/k19042397/miniconda2/envs/adVNTR/bin/advntr", line 11, in sys.exit(main()) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/advntr/main.py, line 134, in main genotype(args, genotype_parser) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/advntr_commands.py, line 124, in genotype genome_analyzier.find_repeat_counts_from_alignment_file(input_file, average_coverage, update) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/advntr/genome_analyzer.py", line 241, in find_repeat_counts_from_alignment_file average_coverage, update) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(*args, **kwargs) File "/users/k19042397/miniconda2/envs/adVNTR/lib/python3.6/site-packages/advntr/vntr_finder.py", line 750, in find_repeat_count_from_alignment_file max_prob=0) # No probability for the estimated genotype TypeError: init() got an unexpected keyword argument 'max_prob'