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) #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) #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!