Please help concoct clustering about anvio

[metehaansever]

Hello @kinosham,
Can you run df -h /tmp to check your disk space. Curious about your usage.
Did you use --tmp-dir-path argument?
To check where is your tempfile
TMPDIR=/Users/your-user-name/Workspace python -c "import tempfile; print(tempfile.gettempdir())"

And also this closed issue may help to find your answer: #906

[kinosham]

So I am able to find the log.txt file now. It coming up with this : # DATE: 16 May 24 10:21:07 # CMD LINE: concoct --coverage_file /nlustre/users/kinosha/tmpmsu4obn3/contig_coverages.txt --composition_file /nlustre/users/kinosha/tmpmsu4obn3/sequence_contigs.fa --basename /nlustre/users/kinosha/tmpmsu4obn3 --threads 16 Up and running. Check /nlustre/users/kinosha/tmpmsu4obn3/log.txt for progress Traceback (most recent call last): File "/apps/anaconda3-2023.03/envs/anvio-8/bin/concoct", line 90, in <module> results = main(args) File "/apps/anaconda3-2023.03/envs/anvio-8/bin/concoct", line 37, in main transform_filter, pca = perform_pca( File "/apps/anaconda3-2023.03/envs/anvio-8/lib/python3.10/site-packages/concoct/transform.py", line 5, in perform_pca pca_object = PCA(n_components=nc, random_state=seed).fit(d) File "/apps/anaconda3-2023.03/envs/anvio-8/lib/python3.10/site-packages/sklearn/base.py", line 1474, in wrapper return fit_method(estimator, *args, **kwargs) File "/apps/anaconda3-2023.03/envs/anvio-8/lib/python3.10/site-packages/sklearn/decomposition/_pca.py", line 428, in fit self._fit(X) File "/apps/anaconda3-2023.03/envs/anvio-8/lib/python3.10/site-packages/sklearn/decomposition/_pca.py", line 483, in _fit X = self._validate_data( File "/apps/anaconda3-2023.03/envs/anvio-8/lib/python3.10/site-packages/sklearn/base.py", line 608, in _validate_data self._check_feature_names(X, reset=reset) File "/apps/anaconda3-2023.03/envs/anvio-8/lib/python3.10/site-packages/sklearn/base.py", line 469, in _check_feature_names feature_names_in = _get_feature_names(X) File "/apps/anaconda3-2023.03/envs/anvio-8/lib/python3.10/site-packages/sklearn/utils/validation.py", line 2229, in _get_feature_names raise TypeError( TypeError: Feature names are only supported if all input features have string names, but your input has ['int', 'str'] as feature name / column name types. If you want feature names to be stored and validated, you must convert them all to strings, by using X.columns = X.columns.astype(str) for example. Otherwise you can remove feature / column names from your input data, or convert them all to a non-string data type.

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On Wed, May 15, 2024 at 3:35 PM Metehan Sever ***@***.***> wrote: Hello @kinosham <https://github.com/kinosham>, Can you run df -h /tmp to check your disk space. Curious about your usage. Did you use --tmp-dir-path argument? To check where is your tempfile TMPDIR=/Users/your-user-name/Workspace python -c "import tempfile; print(tempfile.gettempdir())" And also this closed issue may help to find your answer: #906 <#906> — Reply to this email directly, view it on GitHub <#2266 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKSQVCLMWHL65CENYEX4AD3ZCNQDPAVCNFSM6AAAAABHYDXDYSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJSGU2TIMRSGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[metehaansever]

This error looks related with sklearn's version.
Can you create another environment with all the anvio dependencies and install sklearn version 1.1.*
pip install scikit-learn~=1.1.0
We recently updated sklearn package with py10 migration.
So I am not really sure if its gonna work with anvi-cluster-contigs.

[metehaansever]

#2154 Solution described here.