Hi, I'm looking to install RepeatMasker for use with the Maker and/or RepeatModeler programs. I have installed RepeatMasker and will be using rmblast. I have downloaded the libraries from Repbase (GIRI), and run ./configure in the RepeatMasker folder:
Congratulations! RepeatMasker is now ready to use. The program is installed with a the following repeat libraries: Dfam database version Dfam_2.0 RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20181026 Further documentation on the program may be found here: /home/chris/Documents/maker/exe/RepeatMasker/repeatmasker.help
It suggests i'm using Dfam_Consensus 2017-01-27 and RepBase-2018-10-26.
When I try to run:
I get an error:
parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???; BP. " from DE RepbaseID: SNAP-OL2XX at ./RepeatMasker line 7611.
I'm not sure how to fix this error, as it seems to be a problem with the libraries being generated when configuring RepeatMasker.
I also noticed that when trying to run Repeatmodeler, configuration returns:
WARNING: /home/chris/Documents/maker/exe/RepeatMasker/Libraries/RepeatMasker.lib.[n??] doesn't exist! RepeatModeler will not run correctly without these files. Please re-run /home/chris/Documents/maker/exe/RepeatMasker/configure to create these files automatically. Then re-run this script.
It seems the RepeatMasker.lib file is empty, and configuring RepeatMasker does not change anything.
When I installed the libraries, I unpacked them in the RepeatMasker directory, and seem to have created dfamrepref.embl and RepeatMaskerLib.embl in the libraries directory.
Any help would be greatly appreciated in getting both RepeatMasker (and thus RepeatModeler) up and running!
Additional Info: RepeatMasker Version open-4.0.7 Search engine NCBI/RMBLAST 2.2.27+ Master RepeatMasker Database: /home/chris/Documents/maker/exe/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: dc20170127-rb20181026 )