Error in saving XlsxWriter

[daniquebax]

Hi there,

I encountered an AttributeError while using the CAT (Cluster Alignment Tool) library. The error occurs when attempting to save the results to an Excel file using the save() method in the report.py file.
I am quite new to bioinformatic analyses, so maybe it's a very straight forward solution, but I couldn't figure it out. I posted the output below.

(my_conda_env2)dbax@cn45:/scratch/dbax/CAT$ "/scratch/dbax/CAT/CAT.sh"
[dataset.py->prepare():73]INFO: Preprocessing 1
[dataset.py->_filter_genes():58]INFO: Removing 2 mitochondrial genes
[dataset.py->_filter_genes():58]INFO: Removing 24 ribosomal genes
[dataset.py->prepare():73]INFO: Preprocessing 2
[cat.py->internal_preprocessing():49]INFO: Before 1: (7501, 1974)
[cat.py->internal_preprocessing():50]INFO: Before 2: (71005, 2944)
[cat.py->internal_preprocessing():68]INFO: After 1: (7501, 638)
[cat.py->internal_preprocessing():69]INFO: After 2: (71005, 638)
/vol/mbconda/dbax/my_conda_env2/lib/python3.10/site-packages/scanpy/preprocessing/_normalization.py:233: UserWarning: Some cells have zero counts
  warn(UserWarning("Some cells have zero counts"))
100%|████████████████████████████████████████████████████████████████████████████████████████████████| 1000/1000 [04:51<00:00,  3.43it/s]
[cat.py->run():222]INFO: Saving results to ./results/ds1-vs-ds2
Traceback (most recent call last):
  File "/vol/mbconda/dbax/my_conda_env2/bin/catcli", line 8, in <module>
    sys.exit(main())
  File "/vol/mbconda/dbax/my_conda_env2/lib/python3.10/site-packages/cat/__main__.py", line 110, in main
    run(args)
  File "/vol/mbconda/dbax/my_conda_env2/lib/python3.10/site-packages/cat/cat.py", line 224, in run
    save_tables(tables, output=args.output, dashboard=dashboard)
  File "/vol/mbconda/dbax/my_conda_env2/lib/python3.10/site-packages/cat/report.py", line 126, in save_tables
    writer.save()
AttributeError: 'XlsxWriter' object has no attribute 'save'. Did you mean: '_save'?

Thank you for your attention to this matter. Please let me know if you need any further information or assistance.

Best,
Danique

[matq007]

Hi Danique, could you please try installing lower version of pandas<2 ? I think that is the issue.