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Supplementary. 2: Troubleshooting

1. RuntimeError: Resource exhausted: Out of memory

  • If you are to encounter the message "RuntimeError: Resource exhausted: Out of memory" , add the following variables to the slurm script
  • For module based runs ( version 2.3.2 and above) 
    export TF_FORCE_UNIFIED_MEMORY=1
export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0
  • For Singularity container based runs 
    export SINGULARITYENV_TF_FORCE_UNIFIED_MEMORY=1 
export SINGULARITYENV_XLA_PYTHON_CLIENT_MEM_FRACTION=4.0

2. ValueError: Invalid character in the sequence: n

This will get triggered in the event where an input file doesn't obey the following conditions

  • AlphaFold expects an input query sequence with capitalized one-letter amino-acid types from this set:
 'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 
 'S', 'T', 'W', 'Y', 'V'
  • For monomer runs: Input file for the AlphaFold system should only contain one protein.