Plugin error from diversity: Invalid shape in axis 0

[e_flat_minor (Jonas)]

Hello,

I have been following the moving pictures tutorial with my own data and everything worked fine until I reached the core-metrics-step.

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table /Users/administrator/Desktop/skin3/filtered_table.qza
–p-sampling-depth 40000
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results

Plugin error from diversity:

Invalid shape in axis 0: 0.

Debug info has been saved to /var/folders/lh/ld9r0p7s3p357m6kcksvv4j00000gp/T/qiime2-q2cli-err-ds90x_md.log

I already tried the qiime fragment-insertion filter-features Option to clean sequences from the table which are not present in my tree, yet I experience this error.
What does it mean?

The problems seems to be the rooted-tree, since I can calculate shannon’s diversity with the table.qza and checked the metadata-file for errors.

How can I check my rooted-tree for errors? In fact, I only have one sample/ sequence so far in my pipeline - could this be the error?

Thank you very much in advance!

[Nicholas_Bokulich]

Hi @e_flat_minor,
We cannot tell where this error is coming from if you do not include the full error message (see the log file, or use the --verbose flag when running commands to generate the full error message in your terminal). But your description makes the problem pretty clear (I think).

How can I check my rooted-tree for errors?

You could use qiime tools export to export to newick, then check with a text editor. I am not sure the tree is the issue, though. See below:

I only have one sample/ sequence so far in my pipeline - could this be the error?

That is probably the problem. Many of the analyses in the core-metrics pipeline really only make sense if you have multiple samples, so I would discourage you from using this action (even if we debugged this specific issue, you will run into others).

Good luck!

[e_flat_minor (Jonas)]

Hello @Nicholas_Bokulich,

thank you for your reply. Verbose gives me this error log (see below). I think you are right - e.g. calculating beta-diversity is impossible with only one sample. I will retry once I collected more sequences.

Thank you for your helpful reply.

/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/validation.py:595: DataConversionWarning: Data with input dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in true_divide
proportion_explained = eigvals / sum_eigenvalues
/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/emperor/core.py:614: RuntimeWarning: invalid value encountered in true_divide
c_data = (coords / np.max(np.abs(coords)))
Traceback (most recent call last):
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-375>”, line 2, in core_metrics_phylogenetic
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 458, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_core_metrics.py”, line 59, in core_metrics_phylogenetic
metric=‘unweighted_unifrac’, n_jobs=n_jobs)
File “</Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-465>”, line 2, in beta_phylogenetic
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_beta/_method.py”, line 105, in beta_phylogenetic
variance_adjusted=variance_adjusted, bypass_tips=bypass_tips)
File “/Users/administrator/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/unifrac/_methods.py”, line 103, in unweighted
variance_adjusted, 1.0, bypass_tips, threads)
File “unifrac/_api.pyx”, line 83, in unifrac._api.ssu
File “stringsource”, line 251, in View.MemoryView.array_cwrapper
File “stringsource”, line 153, in View.MemoryView.array.cinit
ValueError: Invalid shape in axis 0: 0.

Plugin error from diversity:

Invalid shape in axis 0: 0.

See above for debug info.