Troubleshooting

Troubleshooting & Environment Setup

Important

If you encounter errors, please ensure you are in the correct working directory. You can verify this by checking the path requirements at the start of the wiki commands you are following. If you have difficulties, please reach out to us for support.

🛠 Environment Activation

If you see a command not found error, you need to initialise the specific environment for that tool. Match your error to the resolution below:

1. REAT

   If you are unable to run reat:

   # Command 'reat' not found
   # Error: seqkit: command not found
   activate_reat

2. Minos

   If you are unable to run minos:

   # Error: minos: command not found
   activate_minos

3. Lifton

   If you are unable to run lifton:

   # Error: lifton: command not found
   activate_lifton

4. BRAKER3

   If you are unable to run braker.pl:

   # Error: braker.pl: command not found
   activate_braker3

🔴 Data recovery

If your working directory becomes corrupted or is accidentally deleted, you may still be able to recover your data by following the guide below.

ℹ️ Guacamole data locations