vinisalazar / metaphor

Metaphor: a general-purpose workflow for assembly and binning of metagenomes
https://metaphor-workflow.readthedocs.io/
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Feature names problem when running concoct #37

Closed francesco-ricci closed 1 year ago

francesco-ricci commented 1 year ago

Hello,

I am having an issue when metaphor runs concoct:

Up and running. Check /data/francesco/analyses/deepsea_coral/cyano_project/metagenome_analysis/metaphorCallorgia/output/binning/concoct/cobinning/log.txt for$ Traceback (most recent call last): File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4/bin/concoct", line 90, in results = main(args) File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4_/bin/concoct", line 37, in main transform_filter, pca = performpca( File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4/lib/python3.10/site-packages/concoct/transform.py", line 5, in perfor$ pca_object = PCA(n_components=nc, randomstate=seed).fit(d) File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4/lib/python3.10/site-packages/sklearn/decomposition/_pca.py", line 435$ self.fit(X) File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4/lib/python3.10/site-packages/sklearn/decomposition/_pca.py", line 485$ X = self._validatedata( File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4/lib/python3.10/site-packages/sklearn/base.py", line 518, in _validate$ self._check_featurenames(X, reset=reset) File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4/lib/python3.10/site-packages/sklearn/base.py", line 385, in _check_fe$ feature_names_in = _get_featurenames(X) File "/data/francesco/metaphor/metaphor/config/conda/9d03e8773574f76122db090afb085ec4/lib/python3.10/site-packages/sklearn/utils/validation.py", line 1893,$ 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$

Thanks for your help!

vinisalazar commented 1 year ago

Hi @francesco-ricci,

Thank you for reporting this issue. Apparently this is a downstream problem of https://github.com/BinPro/CONCOCT/issues/321.

It was fixed by 7597983cdf2b3fafdbe3b6019091f8fc0100ca0a which is included in the current version v1.7.1.

Best, Vini