RepeatModeler No families identified

Question

[kapeelc]

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

[Mehmet]

Hi

When I used these;

A) make a database

/bin/RepeatModeler/BuildDatabase -name mydatabase my.genome.fa

B) Run database

/bin/RepeatModeler/RepeatModeler -database mydatabase

output of RepeatModeler:

consensi.fa.classified

[hlucasnunes]

Did You found how to fix it ? I'm having the same problem !!! : (((