recover from round-6

[XuanZhang-Black]

Hi! I ran RepeatModeler for a 700Mb lepidoptera genome. But the program was terminated by the administrator before the round-6 was finished because the server upgrade. Then I tried to add "-recoverDir RM_238134. SunJul*" for recovery, and I got "This directory (RM_238134. SunJul*) appears to contain a successful run of RepeatModeler. If this is not the case, please report this as a bug at the RepeatMasker website (www.repeatmasker.org)".
My round-6 hasn't finished running yet, although it produced the consensi.fa file, so I wonder how to recover RepeatModeler from round-6?
Is it possible to move the consens.fa and families.stk files out of the round-6 folder?

Best Wishes!

Sincerely,
Xuan Zhang

[rmhubley]

Oh that's unfortunate. The recovery is not written to handle a partial round. Instead it simply repeats the last round again. You could get it to do that by simply moving your round-6 directory to say "round-6.bak", make a new empty "round-6" directory, and retry the recover option. Obviously this is going to redo the entire search for round-6.