Repeatmodeler/Repeatmasker Error

Question

[User 1665]

Hi, I'm trying to use RepeatModeler in the de novo identification of repeats in a newly-sequenced species. RepeatMasker is a prerequisite for RepeatModeler to work. Configuration of RepeatModeler produces the warning message

''WARNING: /RepeatMasker/Libraries/RepeatMasker.lib.[n??] doesn't exist! RepeatModeler will not run correctly without these files. Please re-run /RepeatMasker/configure to create these files automatically. Then re-run this script.''

However, I have configured RepeatMasker and RepeatMasker.lib was generated. I don't know what is '[n??]'. Plus RepeatMasker is perfectly working and masked the known repeats in the query sequence (when it was used independently). Does anyone have experience with such a problem and wants to help?? Thanks

Answer 1

[Eric Fournier]

I'm only guessing, but [n??] sounds like the extensions of files generated by formatdb when creating nucleotide database. Given that RepeatMasker.lib is a FASTA file, maybe you need to run formatdb on it.

[Razzmataz]

I know RECON (one of RepeatModeler's programs) is dependent on BLAST-ing the sequence you are searching in for repeats. It could be doing an early blast for known sequences in building the repeat library, hence the likely need to run formatdb on the RepeatMasker.lib file.