Hello
I have queries regarding taxanomy analysis. when I performed taxanomy analysis with SILVA_132_QIIME_release. I am getting the following errror continously
If I perform taxanomy analysis with customized database also, I am getting that white space error
Herewith I have attached taxonomy analysis result file link also for your perusal
https://drive.google.com/drive/folders/1D-ZGbMA7TKWjgljara8IOksJbk5iHDXR?usp=sharing
Could anyone give suggestion how to rectify this error?
Hi @Asha1,
The error message is pretty clear: It looks like you have a white space in your taxonomy file. I would search for white spaces in your taxonomy files and strip them out either manually by finding and replacing them or using a "strip" functionality in R or Python.
Best,
Justine
Hi
After removing white space also, I am getting error again
I have attached files link for your perusal
https://drive.google.com/drive/folders/1D-ZGbMA7TKWjgljara8IOksJbk5iHDXR?usp=sharing
kindly help me how to solve this error?
Hi @Asha1,
Could you please share the contents fo the debug file? Post it as text, rather than attaching it.
Best,
Justine
Thank so much for ur prompt reply. I have given debug file error and files for your perusal.
(qiime2-2019.1) ruthra@bioinformatics-PowerEdge-T630:~/miniconda2/envs/qiime2-2019.1/v3-v4_region_result/99/manoj/cd_result$ qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads single.qza --i-reference-taxonom
y cd.qza --o-classifier classifier.qza --verbose
/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_feature_classifier/classifier.py:101: UserWarning: The TaxonomicClassifier artifact that results from this method was trained using scikit-learn version 0.
20.2. It cannot be used with other versions of scikit-learn. (While the classifier may complete successfully, the results will be unreliable.)
warnings.warn(warning, UserWarning)
Traceback (most recent call last):
File “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-340>”, line 2, in fit_classifier_naive_bayes
File “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/ruthra/miniconda2/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 “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_feature_classifier/classifier.py”, line 316, in generic_fitter
pipeline)
File “/home/ruthra/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_feature_classifier/_skl.py”, line 31, in fit_pipeline
y, X = list(zip(*data))
ValueError: not enough values to unpack (expected 2, got 0)
Plugin error from feature-classifier:
not enough values to unpack (expected 2, got 0)
cd.txt (3.5 KB)
file link https://drive.google.com/drive/folders/1QjadmGT9C-WS44jj8Oizxc1MGykjwvVB?usp=sharing
Thanking you once again for your suggestions and help. Looking forward to your reply
@Asha1,
Your taxonomy database is not formatted properly. See this post (and others in the forum archive with the search functionality) for help troubleshooting:
Good luck!
