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  • Replace non-blocking subprocess calls with subprocess.run()
  • Ensure RNAfold completes before file operations
  • Add proper error handling for process execution
  • Fixes file not found errors when processing long sequences

- Replace non-blocking subprocess calls with subprocess.run() 
- Ensure RNAfold completes before file operations
- Add proper error handling for process execution
- Fixes file not found errors when processing long sequences
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