Does RM behave differently on softmasked input?

[Rik-149]

I accidentally used softmasked input for RM. The lettuce Salinas_v11 assembly from NCBI has already been softmasked but this is not mentioned anywhere so I assumed it was unmasked.

I'd like to know wheter RM behaves any differently when you provide softmasked input or if it would be wise to re-run the RM step.

I need to compare the output to multiple other assemblies that were not softmasked prior to RM.

Thanks in advance
P.S. RepeatModeler has been very useful thank you for developing it