Troubleshooting
Procedure 1A
PyCoGAPS
| Step | Problem | Possible Reason | Solution |
|---|---|---|---|
| 1 | Error with cloning repository due to large files (inputdata.h5ad, cogapsresult.h5ad) | Git LFS (large file storage) is not installed. | Run the following command: brew install git-lfs |
| 2 | No module named pybind11 | pybind11 was not successfully installed | If using conda, run: conda install -c conda-forge pybind11 Otherwise, run: pip install pybind11 |
| 2 | src/bindings.cpp:1:10: fatal error: ‘CoGAPS/src/GapsRunner.h’ file not found #include “CoGAPS/src/GapsRunner.h” ^~~~~~~~~~~~~~~~~~~~~~~~~ 1 error generated. error: command ‘gcc’ failed with exit status 1 | CoGAPS library was not downloaded | Make sure you use –recursive flag when installing pycogaps. git clone https://github.com/FertigLab/pycogaps.git –recursive |
| 11 | Runtime is prohibitively long, given reasonable scales of data (typical timing is as given in n*log(n)). | If run times 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 1B
PyCoGAPS in Docker
| Step | Problem | Possible Reason | Solution |
|---|---|---|---|
| 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 |
| 8 | ModuleNotFoundError: No module named ‘analysis_functions’ | analysis_functions.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 2
R CoGAPS
| Step | Problem | Possible Reason | Solution |
|---|---|---|---|
| 8 | Runtime is prohibitively long, given reasonable scales of data (typical timing is as given in n*log(n)). | If run times 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 3
GenePattern Notebook
| Step | Problem | Possible Reason | Solution |
|---|---|---|---|
| Step 6 | FileNotFoundError | Data file not uploaded to project folder. | Go to the project folder, and click ‘Upload’ to upload your file to the folder. |
| Step 6 | 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. |