[go: nahoru, domu]

Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cyanoseq database in Qiime2 #3

Open
Listen-Lii opened this issue Jun 10, 2023 · 2 comments
Open

Cyanoseq database in Qiime2 #3

Listen-Lii opened this issue Jun 10, 2023 · 2 comments

Comments

@Listen-Lii
Copy link

Thank you for developing the Cyanoseq database, which is very helpful for aquatic microbial research. I want to use Cyanoseq database on my 16S rRNA gene amplicon sequencing data. I downloaded CyanoSeq_1.2_SILVA138.1_QIIME2_classifier.qza and found it is a trained database. So, I run these codes in Qiime2:

qiime feature-classifier classify-sklearn
--i-reads zotus.fa.qza
--i-classifier CyanoSeq_1.2_SILVA138.1_QIIME2_classifier.qza
--o-classification taxonomy.qza
But there is an error: Plugin error from feature-classifier: 0.

Here are messages in debug log file:

Traceback (most recent call last):
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in classify_sklearn
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/site-packages/qiime2/sdk/action.py", line 223, in bound_callable
callable_args[name] = artifact._view(
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/site-packages/qiime2/sdk/result.py", line 373, in _view
result = transformation(self._archiver.data_dir)
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/site-packages/q2_feature_classifier/_taxonomic_classifier.py", line 72, in _1
pipeline = joblib.load(os.path.join(dirname, 'sklearn_pipeline.pkl'))
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 587, in load
obj = _unpickle(fobj, filename, mmap_mode)
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 506, in _unpickle
obj = unpickler.load()
File "/share/soft/miniconda3/envs/qiime2202208/lib/python3.8/pickle.py", line 1212, in load
dispatchkey[0]
KeyError: 0

Qiime2 works well when using other reference database with the same data. So, I think there may be some problems with the file CyanoSeq_1.2_SILVA138.1_QIIME2_classifier.qza. Can you fix this?

Thank you very much for your reply and suggestions.

@Apatzingan1
Copy link

Maybe the compatibility whit the Qiime version, actually working in qiime2-2023.5 and it runs smoothly

@Listen-Lii
Copy link
Author
Listen-Lii commented Jul 31, 2023

Thank you very much, I used qiime2-2023.5 and now it works!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants