Disabling safety checks - amkozlov/raxml-ng GitHub Wiki

Option: --force [ <checks> ]

Example: raxml-ng --msa ali.fa --model GTR+G --force

Example: raxml-ng --msa ali.fa --model GTR+G --force msa,model_overfit

Example: raxml-ng --msa ali.fa --model GTR+G --threads 16 --force perf_threads

If you know what you're doing, you can disable all or some of the RAxML-NG builtin safeguards with the --force option:

Command	Meaning
--force perf_threads	Do not check for minimum number of alignment patterns per thread.
--force perf	Disable all performance-related checks listed above.
--force msa_names	Do not check for invalid characters in sequence names.
--force msa_dups	Do not check for duplicate sequences.
--force msa_allgaps	Do not check for sequences and columns consisting entirely of missing data (gaps).
--force msa_extra_cols	Do not require that all MSA sites are assigned to partitions (i.e., allow site exclusion). (raxml-ng v2.0)
--force msa	Disable all MSA-related checks listed above.
--force model_zero_freqs	Do not check for zero state frequencies.
--force model_invalid_freqs	Do not check for invalid state frequencies (e.g. user-defined state frequencies which do not sum up to one)
--force model_lg4_freqs	Do not warn about non-model state frequencies with LG4M/LG4X (discouraged).
--force model_asc_bias	Do not check for partitions with invariant sites and ascertainment bias enabled.
--force model_overfit	Do not warn about using parameter-rich models with small alignments (overfitting!) .
--force model_rate_scalers	Do not auto-enable rate scalers with >2000 taxa
--force model	Disable all model-related checks listed above.
--force	Disable all safety checks listed above. Use with caution!

The --force option also accepts a comma-separated list of individual checks, e.g. --force msa_dups,msa_allgaps or --force model,perf.