Hi,

I have an assembled genome that I want to use with RepeatModeler v1.01. I started with building the database using

BuildDatabase -name reapmod -engine ncbi ref.fa

Building database reapmod:

Adding ref.fa to database

Number of sequences (bp) added to database: 61 ( 374424240 bp )

next used RepeatModeler

RepeatModeler -engine ncbi -pa 6 -database reapmod

Output tail log:

Element Gathering: 00:00:00 (hh:mm:ss) Elapsed Time Refining family-11278 model... WARNING: Refiner did not return a consensus. Refinement: 00:00:00 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:30 (hh:mm:ss) Elapsed Time Round Time: 48:04:57 (hh:mm:ss) Elapsed Time

Discovery complete: 0 families found Program Time: 81:07:32 (hh:mm:ss) Elapsed Time Working directory: /home/kap12/repeatmodeller/RM_5608.SunDec241842082017 may be deleted unless there were problems with the run. No families identified. Perhaps the database is too small or contains overly fragmented sequences.

I dont seem to have the correct output files. The consensi.fa and families.stk dont have any contents.

My genome size was 364MB, it took me 4-5 days to complete on 4CPU 60Gb RAM instance. Not sure why no families were identifed.

Any help appreciated

Thanks Kapeel