11  Troubleshooting

• Wrong input orientation
  Deconvolution commands expect genes × samples. For deside, --transpose can be helpful depending on your file.

• Mixed separators / encoding
  Prefer .csv , .txt or .tsv consistently. Auto‑detection works in most subcommands but you can override with explicit flags where provided.

• DeSide model missing The deside subcommand requires pretrained model files. If you get errors like FileNotFoundError: DeSide_model not found , download the official model archive from: https://figshare.com/articles/dataset/DeSide_model/25117862/1?file=44330255

• Python version for DeSide The deside subcommand runs ONLY on Python 3.9. Other versions (3.8/3.10/3.11/…) are not supported .When invoked via the iobrpy CLI, it automatically creates/uses an isolated virtual environment with pinned dependencies so it doesn’t leak packages from your outer env. You can override the venv location with IOBRPY_DESIDE_VENV or force a clean rebuild with IOBRPY_DESIDE_REBUILD=1; the CLI wires iobrpy into that venv through a small shim and then launches the worker.