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svalkiers / clusTCR

CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results.
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Urgent! Error using clustering.fit #40

Closed cz239 closed 1 year ago

cz239 commented 2 years ago

I got the following error when using the clustering function

Screen Shot 2022-06-02 at 23 35 43

I installed it using the following command and set up the environment:

conda install clustcr -c svalkiers -c bioconda -c pytorch -c conda-forge

conda env create -f env.yml

Could you please take a look at it? Many thanks!

svalkiers commented 2 years ago

Hi, I believe this error results from a version inconsistency with the networkx package. The new syntax for this command is to_scipy_sparse_matrix. I will try to resolve this issue in the next ClusTCR release by updating the networkx version.

For now, you can work around this issue by setting up a fresh conda environment and installing the clustcr package using the conda install clustcr -c svalkiers -c bioconda -c pytorch -c conda-forge command as mentioned. No need to set up the environment manually, all the package dependencies are downloaded with the installation of clustcr.

Alternatively, in your current environment, you can try to remove both clustcr and networkx, and reinstall clustcr subsequently.

Hope this helps.