Troubleshooting¶

Common issues and solutions for ScanMST users.

Installation Issues¶

Python Version Errors¶

Symptom: ModuleNotFoundError: No module named 'scanmst'

Cause: Wrong Python environment or installation failed

Solution:

# Check Python version (must be 3.9 or higher )
python --version

# Verify pip is using correct Python
which pip
python -m pip --version

# Reinstall in current environment
python -m pip install --force-reinstall scanmst

Dependency Conflicts¶

Symptom: Pip reports dependency conflicts during installation

Solution:

# Install in a clean environment
python -m venv scanmst_env
source scanmst_env/bin/activate
pip install scanmst

Runtime Issues¶

BAM File Issues¶

# Check file permissions
ls -l input.bam

# Add read permission
chmod +r input.bam

General Help¶

Enable Verbose Logging¶

For debugging, enable detailed output:

scanmst ... --log-level trace

Check ScanMST Version¶

Ensure you're using the latest version:

# Check current version
scanmst --version

# Update to latest
pip install --upgrade scanmst

System Information¶

Collect system info for bug reports:

# Python version
python --version

# ScanMST version
scanmst --version

Getting Further Help¶

If your issue isn't covered here:

1. Check existing issues: GitHub Issues
2. Search discussions: GitHub Discussions
3. Open a new issue: Include:
4. ScanMST version (scanmst --version)
5. Python version (python --version)
6. Operating system
7. Complete error message
8. Minimal reproducible example