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FofanovLab / VaST

Variant Site Strain Typer: Identifies the minimum number of variable genomic site that are required to resolve a group of related bacterial strains
MIT License
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Error running pattern selection module #3

Closed shashidr closed 5 years ago

shashidr commented 5 years ago

Hi Tara,

I was able to run the preprocessing workflow without errors ( input files generated with NASP), but pattern selection module is giving me the following error. Appreciate any input. Thanks,

Shashi

Command: python VaST-1.0/VaST/pattern_selection.py --log DEBUG -t 32 TEST TEST_2019-01-14_16-12-10/

Traceback (most recent call last): File "VaST-1.0/VaST/pattern_selection.py", line 323, in pattern_selection(PROJECT_DIR, PARAMS) File "VaST-1.0/VaST/pattern_selection.py", line 111, in pattern_selection int(preprocessing_history.get_parameter("PZ_SIZE"))) File "VaST-1.0/VaST/pattern_selection.py", line 23, in _get_minimum_spanning_set for rep, mss in enumerate(minimum_spanning_set_objs)] File "VaST-1.0/VaST/Minimum_Spanning_Set.py", line 91, in get_minimum_spanning_set self._add_pattern_to_set([next_pattern]) File "VaST-1.0/VaST/Minimum_Spanning_Set.py", line 186, in _add_pattern_to_set _ambiguous_score_helper(self._current_resolution) File "VaST-1.0/VaST/Minimum_Spanning_Set.py", line 325, in _ambiguous_score_helper n_strains_in_feature_category = Counter(chain(pattern)) File "/local/anaconda2/envs/vast_env/lib/python2.7/collections.py", line 477, in init self.update(args, kwds) File "/local/anaconda2/envs/vast_env/lib/python2.7/collections.py", line 566, in update for elem in iterable: TypeError: 'float' object is not iterable

tfursten commented 5 years ago

Hi @shashidr, can you try to run it again with the latest version on master and see if you have the same issue?

shashidr commented 5 years ago

Latest version worked fine. Thanks Tara

tfursten commented 5 years ago

@shashidr That's great!