I have met the same issue as described in https://cistem.org/cistem-100-beta-auto-refine-error-after-iteration-1-finish.
I import the STAR file and mrc stack from Relion extraction (with refined angular information included). First, the manual refinement works fine. Then, the auto refinement works fine , too.
However, when I run ab initial model generation and use the resulting model as the reference of auto refinement, the error occurs at the second iteration:
Error: File '/dev/null' couldn't be removed (error 13: Permission denied)
Error: Number of particles selected = 0; please change score threshold
float FrealignParameterFile::ReturnThreshold(float, bool)
Any suggestions? Thanks in advance!!