-recoverDir option useless because round-1 apparently failed

[marcopessoa]

This is the same issue reported previously (#21). I am running RepeatModeler version 2.0, just released.

The round-1 directory does not contain consensi.fa and sampleDB-1.fa.rscons.filtered is empty. In addition, repeatscout.log is empty as well and filter-stage-1.log says

/usr/local/bin/filter-stage-1.prl: No such file or directory

Although round-1 fails the pipeline continues. I found a problem with LTR_retriever and it would be great to resume the pipeline from that point and not from the start.

Where should I look for filter-stage-1.prl to put it in the right location?

[jebrosen]

filter-stage-1.prl is part of RepeatScout. It looks like the configuration system does not check for that file but it could (it currently only checks for RepeatScout and build_lmer_table).

What method did you use to install RepeatScout that didn't include that file?

[marcopessoa]

Ok, I've just found filter-stage-1.prl in the RepeatScout directory. I will fix my paths and try again. Thanks!

EDIT: And yes, I guess it would be nice for the configuration file to check for it. I would never have guessed RepeatScout didn't run in round-1 if it wasn't for the behavior of -recoverDir.