Param CSV file construction for cellranger reanalyze pipeline

[Ankita-1211]

Hi

I am trying to run cellranger reanalyze pipeline with my --params .

I am passing giving below arguments in my CSV file

num_principal_comps,10 cbc_knn,10 cbc_alpha,0.1 cbc_sigma,150 cbc_realign_panorama,FALSE graphclust_neighbors,0 neighbor_a,-230 neighbor_b,120 max_clusters,10 tsne_perplexity,30 tsne_theta,0.5 tsne_max_dims,2 tsne_max_iter,1000 tsne_stop_lying_iter,250 tsne_mom_switch_iter,250 umap_n_neighbors,30 umap_max_dims,2 umap_min_dist,0.3 umap_metric,correlation random_seed,0

but I am getting error or umap_metric argument which says

[error] Pipestance failed. Error log at: reanalyze_out/SC_RNA_REANALYZER_CS/SC_RNA_ANALYZER/RUN_UMAP/fork0/chnk0-u21f5dabd90/_errors

Log message: Traceback (most recent call last): File "/home/ec2-user/tools/cellranger-6.0.1/lib/python/cellranger/analysis/lm_umap.py", line 70, in run_umap transformed_umap_matrix = umap_reducer.fit_transform(transformed_pcamatrix) File "/home/ec2-user/tools/cellranger-6.0.1/external/anaconda/lib/python3.7/site-packages/umap/umap.py", line 1596, in fittransform self.fit(X, y) File "/home/ec2-user/tools/cellranger-6.0.1/external/anaconda/lib/python3.7/site-packages/umap/umap.py", line 1373, in fit self._validateparameters() File "/home/ec2-user/tools/cellranger-6.0.1/external/anaconda/lib/python3.7/site-packages/umap/umap.py", line 1307, in _validate_parameters raise ValueError("metric must be string or callable") ValueError: metric must be string or callable

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/ec2-user/tools/cellranger-6.0.1/external/martian/adapters/python/martian_shell.py", line 659, in _main stage.main() File "/home/ec2-user/tools/cellranger-6.0.1/external/martian/adapters/python/martian_shell.py", line 618, in main self._run(lambda: self._module.main(args, outs)) File "/home/ec2-user/tools/cellranger-6.0.1/external/martian/adapters/python/martian_shell.py", line 589, in _run cmd() File "/home/ec2-user/tools/cellranger-6.0.1/external/martian/adapters/python/martian_shell.py", line 618, in self._run(lambda: self._module.main(args, outs)) File "/home/ec2-user/tools/cellranger-6.0.1/mro/rna/stages/analyzer/run_umap/init.py", line 142, in main random_state=args.random_seed, File "/home/ec2-user/tools/cellranger-6.0.1/lib/python/cellranger/analysis/lm_umap.py", line 85, in run_umap transformed_umap_matrix = umap_reducer.fit_transform(transformed_pcamatrix) File "/home/ec2-user/tools/cellranger-6.0.1/external/anaconda/lib/python3.7/site-packages/umap/umap.py", line 1596, in fittransform self.fit(X, y) File "/home/ec2-user/tools/cellranger-6.0.1/external/anaconda/lib/python3.7/site-packages/umap/umap.py", line 1373, in fit self._validateparameters() File "/home/ec2-user/tools/cellranger-6.0.1/external/anaconda/lib/python3.7/site-packages/umap/umap.py", line 1307, in _validate_parameters raise ValueError("metric must be string or callable") ValueError: metric must be string or callable

Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure.

Shutting down.

could you please guide how to pass this particular argument.in csv file for reanalyzed analysis?

[evolvedmicrobe]

Hi @Ankita-1211, This error is caused by the metric being encoded as bytes instead of strings. Easiest option to solve your problem would be to delete the line umap_metric,correlation from your file as correlation is the default metric in use.

[Ankita-1211]

How about if I want to change correlation to any other method as given in this page https://umap-learn.readthedocs.io/en/latest/parameters.html#metric? How do we pass that in this csv file.

[Ankita-1211]

Hi @Ankita-1211, This error is caused by the metric being encoded as bytes instead of strings. Easiest option to solve your problem would be to delete the line umap_metric,correlation from your file as correlation is the default metric in use.

How about if I want to change correlation to any other method as given in this page https://umap-learn.readthedocs.io/en/latest/parameters.html#metric? How do we pass that in this csv file.

[evolvedmicrobe]

If you'd like to use another option, the easiest path will be to edit the code to prevent it from being converted to binary.

If you open up the file /home/ec2-user/tools/cellranger-6.0.1/lib/python/cellranger/analysis/lm_umap.py and change line 53 so that metric = metric.encode("utf-8") is converted to metric = metric (delete the encode method call).