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.
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'
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