Table 4 |.
Troubleshooting table
| Step | Problem | Possible reason | Solution |
|---|---|---|---|
| Procedure 1, Step 1 | Error with cloning repository due to large files (inputdata.h5ad, cogapsresult.h5ad) | Git large file storage (LFS) is not installed | Run the following command: brew install git-lfs or disable git-lfs and instead download files from https://zenodo.org/record/7709664 |
| Procedure 1, Step 3 | Upon running setup.py, receive the error message: No module named pybind11 | pybind11 was not successfully installed | pip install pybind11. If using conda, run: conda install -c conda-forge pybind11 |
| Upon running setup.py, a ‘file not found’ error for a CoGAPS header file is displayed | CoGAPS library was not downloaded | Make sure you use --recursive flag when cloning pycogaps | |
| Procedure 1, Step 12 | Runtime is prohibitively long, given reasonable scales of data (typical timing is as given in n*log(n)) | If runtimes are prohibitive within reasonable scales of data, this may result from algorithm overfitting zeros | We recommend filtering the data only to genes that are reasonably expressed or filtering to a limited subset of genes (e.g., high variance) |
| Procedure 2, Step 1 | Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running? | Docker is not started up/running | Open the Docker application or run the following command: docker run -d -p 80:80 docker/getting-started |
| Procedure 2, Step 8 | ModuleNotFoundError: no module named ‘analysis_functions’ | analysis_function s.py file is not in the same directory as your new Python file | Make sure analysis_functions.py and your new Python file for calling the functions are in the same directory |
| Procedure 3, Step 8 | Runtime is prohibitively long, given reasonable scales of data (typical timing is as given in n*log(n)) | If runtimes are prohibitive within reasonable scales of data, this may result from algorithm overfitting zeros | We recommend filtering the data only to genes that are reasonably expressed or filtering to a limited subset of genes (e.g., high variance) |
| Procedure 4, Step 6 | FileNotFoundError | Data file not uploaded to project folder | Go to the project folder, and click ‘Upload’ to upload your file to the data folder |
| Error after running the PyCoGAPS cell | Path parameter not updated | Make sure to replace the default path parameter with the ‘Upload’ button to upload your data |