Jeb Rosen

Sorry for the long wait. By my estimate, the latest version of RepBase RepeatMasker Edition (which may be different from 20170127) includes about 2000 more repeat families than Dfam (counting...

It looks like this is because there are multiple taxa with the same name (Drosophila is both a genus and a subgenus; Anopheles is a genus, subgenus, and series). RepeatMasker...

You should have a file named `rmblastdb.log` at `/scratch/software/RepeatMasker-4.1.0/RepeatMasker/Libraries/CONS-Dfam_3.1/general`. If you could post the contents of that file, that would help greatly with troubleshooting this.

Can you try deleting or renaming `CONS-Dfam_3.1` to something else, like `CONS-Dfam_3.1.old`? `RepeatMasker` will regenerate it the next time. I did some digging, and the `No locks available` message is...

That's unfortunate - I expect it will be pretty difficult for us to reproduce, fix, or work around this ourselves. There are a few potential workarounds: * Make the `RepeatMasker/Libraries`...

> 1. For lines 1 to 3, the parentheses are in column 14 , but for lines 4 and 5 on column 12. This is normal in RepeatMasker's `.out` format....

@githubgig You can send files to me at `[email protected]`, or Robert at `[email protected]`. The files might be too big for an email attachment; if that is the case we can...

Thank you for sending those! I have a few ideas of why these negative coordinates might have been produced, and I will reach out again here and/or by email when...

From the error messages it looks like you have files from multiple versions of RepeatMasker mixed together - in this case, `RMRBMeta.embl` should have been updated and `queryRepeatDatabase.pl` should have...

Hm, what do you get from this command? `ls -l /Users/ohon_ad/Documents/Tools/RepeatMasker/RepeatMasker_4.1.1/Libraries/RepeatMaskerLib.h5`