Hello,

I have been running RepeatModeler on my de novo assembled genome. I have run it multiple times and it runs for about 4-5 days and completes with the expected consensi.fa.classified output file. However, the LTR run, which should generate another fasta in a separate folder, outputs the following:

LTR Structural Analysis
=======================
Running LtrHarvest...LtrPipeline: GenomeTools failed to build suffixtree datastructure.  This is frequently
             caused by a lack of disk space. Error code: 65536
LTRPipeline: No results returned from LTR structural finder ( LtrHarvest ).
LTRPipeline Time: 00:00:21 (hh:mm:ss) Elapsed Time

I have ran on larger nodes and set the tmp directory to a location with unlimited space.

1. Has anyone encountered this error before and how did they resolve it?
2. Is there a way I can run LTR Harvest separately from the RepeatModeler run so I don't have to wait 4 days for a result?