Longitudinal linear-mixed-effects syntax error


#1

Hi,
I have a similar issue as reported (but not solved?) here:

Continuing the discussion from Qiime longitudinal linear-mixed-effects issue:

The command I used is the following:

qiime longitudinal linear-mixed-effects --m-metadata-file metadatafile_amplicons_resistome_v2.txt --m-metadata-file Metagenome_Amplicons_silva119_274bp_e2000_bc_pcoa.qza --p-metric ‘Axis 1’ --p-group-columns relative_air_humidity,air_temperature_C,confinement,environment_feature --p-state-column sea_level --p-individual-id-column grouping --o-visualization 02_longitudinal/Metagenome_Amplicons_LME_state_sea_level.qzv --verbose

And the error message is:

Traceback (most recent call last):
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in linear_mixed_effects
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 424, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/q2_longitudinal/_longitudinal.py”, line 161, in linear_mixed_effects
individual_id_column, random_effects=random_effects)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/q2_longitudinal/_utilities.py”, line 348, in _linear_effects
re_formula=random_effects)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/statsmodels/regression/mixed_linear_model.py”, line 935, in from_formula
exog_vc=exog_vc, groups=groups, *args, **kwargs)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/statsmodels/base/model.py”, line 155, in from_formula
missing=missing)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/statsmodels/formula/formulatools.py”, line 65, in handle_formula_data
NA_action=na_action)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/highlevel.py”, line 310, in dmatrices
NA_action, return_type)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/highlevel.py”, line 165, in _do_highlevel_design
NA_action)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/highlevel.py”, line 70, in _try_incr_builders
NA_action)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/build.py”, line 689, in design_matrix_builders
factor_states = _factors_memorize(all_factors, data_iter_maker, eval_env)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/build.py”, line 354, in _factors_memorize
which_pass = factor.memorize_passes_needed(state, eval_env)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/eval.py”, line 474, in memorize_passes_needed
subset_names = [name for name in ast_names(self.code)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/eval.py”, line 474, in
subset_names = [name for name in ast_names(self.code)
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/site-packages/patsy/eval.py”, line 105, in ast_names
for node in ast.walk(ast.parse(code)):
File “/home/data/galaxy_tool_dependencies/_conda/envs/[email protected]/lib/python3.5/ast.py”, line 35, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File “”, line 1
Axis 1
^
SyntaxError: invalid syntax

Plugin error from longitudinal:

invalid syntax (, line 1)

See above for debug info.

Looking forward to get some help!
Cheers!


(Matthew Ryan Dillon) assigned Nicholas_Bokulich #2

(Nicholas Bokulich) #3

It looks like you are running the 2018.8 release — could you please update to the latest version (2018.11) and try again? That release had some changes that should fix this — but indeed, I never heard back from the user on that other thread to properly debug this so the changes made in 2018.11 might not work for that particular use case.


(Nicholas Bokulich) unassigned Nicholas_Bokulich #4

#5

Hi Nicholas,
Just to let you know…
After updating to version 2018.11 and some further troubleshooting due to low variances everything worked. :slight_smile:
Thanks for your support!


(system) closed #6

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