Issue:I get an IndexError when I try to run advntr addmodel. What can be done to fix this error?
Version:
adVNTR 1.3.3 (downloaded using conda)
(Note: I have tried to install the latest GitHub version but it fails to build because of a Cython CompileError.)
Searching reference genome for regions with shared kmers with VNTR. It takes a few hours for human genome
Traceback (most recent call last):
File "/home/jeffr/miniconda3/envs/advntr-test/bin/advntr", line 11, in <module>
sys.exit(main())
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/__main__.py", line 138, in main
add_model(args, addmodel_parser)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/advntr_commands.py", line 193, in add_model
scaled_recruitment_score = vntr_finder.train_classifier_threshold(args.reference)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/profiler.py", line 8, in wrapper
retval = func(*args, **kwargs)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/vntr_finder.py", line 687, in train_classifier_threshold
hmm = self.get_vntr_matcher_hmm(read_length=read_length)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/vntr_finder.py", line 87, in get_vntr_matcher_hmm
vntr_matcher = self.build_vntr_matcher_hmm(copies, flanking_region_size)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/profiler.py", line 8, in wrapper
retval = func(*args, **kwargs)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/vntr_finder.py", line 69, in build_vntr_matcher_hmm
vntr_matcher = get_read_matcher_model(left_flanking_region, right_flanking_region, patterns, copies)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/profiler.py", line 8, in wrapper
retval = func(*args, **kwargs)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/hmm_utils.py", line 485, in get_read_matcher_model model = get_suffix_matcher_hmm(left_flanking_region)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/profiler.py", line 8, in wrapper
retval = func(*args, **kwargs)
File "/home/jeffr/miniconda3/envs/advntr-test/lib/python3.6/site-packages/advntr/hmm_utils.py", line 317, in get_suffix_matcher_hmm model.add_transition(unit_start, delete_states[0], delete_error)
IndexError: list index out of range
@mehrdadbakhtiari
Issue: I get an
IndexError
when I try to runadvntr addmodel
. What can be done to fix this error?Version: adVNTR 1.3.3 (downloaded using conda) (Note: I have tried to install the latest GitHub version but it fails to build because of a Cython CompileError.)
Command:
Output: