Hi,
I have run into some trouble when trying to do the q2-quality-control evaluate-composition-pipeline. I have downloaded the expected-taxonomy.tsv file from mocrobiota (mockrobiota/data/mock-21/silva/123/99-otus/expected-taxonomy.tsv at master · caporaso-lab/mockrobiota · GitHub) and followed the Fungal ITS analysis tutorial to convert the .tsv file to a .qza:
biom convert
-i expected-taxonomy1.tsv
-o expected-taxonomy1.biom
--table-type="OTU table"
--to-json
qiime tools import
--type-FeatureTable[RelativeFrequency]
--input-path expected-taxonomy1.biom
--input-format BIOMV100Format
--output-path expected-taxonomy1.qza
expected-taxonomy1.qza (7.6 KB)
I then performed feature-table filter-samples to get a table.qza consisting of my control (mock HM277D) sample only. I renamed the mock-sample to have a sample-id identical to what is found in the expected-taxonomy-file, as it is stated in the ‘Evaluating and controlling data quality with q2-quality-control’ tutorial. I collapsed the sample to level 7 and converted the feature table to relative frequency.
qiime taxa collapse
--i-table table-mock1.qza
--i-taxonomy merged_taxonomy_trained.qza
--p-level 7
--o-collapsed-table table-mock1-collapsed7.qza
qiime feature-table relative-frequency
--i-table table-mock1-collapsed7.qza
--o-relative-frequency-table table-mock1-collapsed7-relative-freq.qza
table-mock1.qza (67.5 KB)
table-mock1-collapsed7.qza (116.5 KB)
table-mock1-collapsed7-relative-freq.qza (121.4 KB)
So far so good
Then I ran the final step
qiime quality-control evaluate-composition
--i-expected-features expected-taxonomy1.qza
--i-observed-features table-mock1-collapsed7-relative-freq.qza
--o-visualization control-evaluate1.qzv
And ended up with the error message as follows:
Plugin error from quality-control:
Invalid RGBA argument: masked
Debug info has been saved to /work/users/ainafos/tmp/qiime2-q2cli-err-b55v6orn.log
(/opt/anaconda3/env/qiime2/2019.10.0) ainafos@bioint01:/work/users/ainafos/Master/MockQC$ cat /work/users/ainafos/tmp/qiime2-q2cli-err-b55v6orn.log
/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/q2_quality_control/_utilities.py:174: FutureWarning: Sorting because non-concatenation axis is not aligned. A future version
of pandas will change to not sort by default.
To accept the future behavior, pass 'sort=False'.
To retain the current behavior and silence the warning, pass 'sort=True'.
obs_collapsed.loc[sample]], axis=1).fillna(0)
Traceback (most recent call last):
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/decorator.py:decorator-gen-200>", line 2, in evaluate_composition
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/qiime2/sdk/action.py", line 445, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/q2_quality_control/quality_control.py", line 76, in evaluate_composition
plot_observed_features_ratio=plot_observed_features_ratio)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/q2_quality_control/_utilities.py", line 112, in _evaluate_composition
results, xval='level', yvals=yvals, palette=palette)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/q2_quality_control/_utilities.py", line 265, in _pointplot_multiple_y
sns.pointplot(data=results, x=xval, y=score, ax=axes, color=color)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/seaborn/categorical.py", line 3340, in pointplot
plotter.plot(ax)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/seaborn/categorical.py", line 1811, in plot
self.draw_points(ax)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/seaborn/categorical.py", line 1757, in draw_points
c=hex_colors, edgecolor=hex_colors)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/init.py", line 1589, in inner
return func(ax, *map(sanitize_sequence, args), **kwargs)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/axes/_axes.py", line 4490, in scatter
alpha=alpha
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/collections.py", line 883, in init
Collection.init(self, **kwargs)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/collections.py", line 128, in init
self.set_edgecolor(edgecolors)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/collections.py", line 728, in set_edgecolor
self._set_edgecolor(c)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/collections.py", line 712, in _set_edgecolor
self._edgecolors = mcolors.to_rgba_array(c, self._alpha)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/colors.py", line 286, in to_rgba_array
result[i] = to_rgba(cc, alpha)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/colors.py", line 177, in to_rgba
rgba = _to_rgba_no_colorcycle(c, alpha)
File "/opt/anaconda3/env/qiime2/2019.10.0/lib/python3.6/site-packages/matplotlib/colors.py", line 238, in _to_rgba_no_colorcycle
raise ValueError("Invalid RGBA argument: {!r}".format(orig_c))
ValueError: Invalid RGBA argument: masked
I have searched the forum for a similar error message, and turned to my friend Google, but I cannot find any such error message connected to QIIME2
I hope you can guide me to the step where I am doing something wrong
Best,
Aina