Troubleshooting

Common Issues

File Not Found Error

Error: FileNotFoundError: [Errno 2] No such file or directory Solution: Ensure all input files (BAM, FASTA, BED) exist and paths are correct. Use absolute paths to avoid ambiguity.

Permission Error

Error: PermissionError: [Errno 13] Permission denied Solution: Check that you have write permissions for the output directory.

Missing Dependencies

Error: ModuleNotFoundError: No module named '...' Solution: Ensure Krewlyzer is installed in your current environment.

uv pip install krewlyzer

Or use the Docker image.

Reference Mismatch

Issue: Results look wrong or empty. Solution: Ensure your BAM files and the reference FASTA are from the same genome build (e.g., both hg19 or both hg38). Krewlyzer defaults to hg19 for provided data files.

Memory Errors

Issue: Process crashes on large BAM files. Solution: Increase available RAM (≥16GB recommended). Reduce the number of threads if running in parallel.