RepeatMasker library out of date.

Question

[The Last Word]

While trying to run RepeatMasker I get the error

The RepeatMasker.lib file is out of date. This version of RepeatMasker requires library version 20140131 or higher. Your version is 20110419.

I am still waiting for a response from Genetic Information Research Institute for a password to login for downloading and using their libraries to run repeatmasker. Would that fix this error?

Also I haven't been able to see the default libraries but I am guessing that it is suitable to be used on any genome when we haven't got our own custom made libraries. Is that so?

[susannehoward]

I have the exact same problem, exact same numbers.

I thought the library mentioned came with the repeatmasker distribution? I have the RepBase19.06.fasta but those have a different file type? Cannot figure how that would replace the repeatmasker.lib?

[The Last Word]

Did you work out a solution?

[florent.risacher]

I know it won't help much but I have the same problem.

I tried using a custom library (that I made) and it still gives me the same error and as Susan mentioned the library comes with the program so I don't know why it would be incompatible.

Answer 1

[susannehoward]

After I received my password from giri I downloaded the new repeatmaster file, unzipped it into the libraries folder that repeatmaster had built and I have had no problems using it since then. I have not however tried to install a custom library yet.

Susanne

[florent.risacher]

It works for me too ! The problem with the custom library is that repeatMasker seems to check for the library version first even if you use a custom one with the function -lib.

[The Last Word]

exactly.. I got it working yesterday which is when I asked you if you found the solution..

[biomagician]

Hi, I have the same problem. Can you please give more details about the steps you made to fix the problem? Where do you download the repeatmasker file from? Where is the libraries folder? How to you install repeatmaser? I used homebrew and hence don't know the detailed steps. Best, Thanks. C.

[jaudall]

Could someone please add specifically 'how' this is done. There is literally no instructions about it. Did you download the file from the giri website or the command line?

At the risk of a little embarrassment, here's why I've tried and I'm finding this process extremely frustrating!

1. I moved the original files (out of date ones) to a different folder and tried to install the new ones. I can't tell what files to download from giri.

The included install libraries files were:

Dfam.hmm
README
RepeatAnnotationData.pm
RepeatMasker.lib
RepeatMasker.lib.nhr
RepeatMasker.lib.nin
RepeatMasker.lib.nsq
RepeatPeps.lib
RepeatPeps.lib.phr
RepeatPeps.lib.pin
RepeatPeps.lib.psq
RepeatPeps.readme
taxonomy.dat

There is nothing similar to this on giri! I downloaded the current files:

RepBase23.05.embl.tar.gz 
RepBaseRepeatMaskerEdition-20170127.tar.gz

and unzipping them produces a lot of *.ref files. I put them in the new Libraries folder, but then it says it can't find "RepeatMasker.lib" or something similar.

The zipped file "RepBaseRepeatMaskerEdition-20170127.tar.gz" produced "RMRBSeqs.embl". I renamed it to RepeatMaskerLib.embl.

2. After running it again, it said I didn't have the taxonomy file. Then I copied the old taxonomy file to the Libraries, and ran it.

3. Then it is saying it doesn't have the genome/is.lib file. It must be making the general folder, because I didn't put it there. So How in the world would I know where to get it? where the hell is the general folder coming from? I put the general files there that a friend had (and his RepeatMaskerLib file), then it said it was out of date again!

Clearly, it shouldn't be this hard! Please someone post the method how to update the libraries. The kicker is the I have my own library and all of this doesn't even matter. I changed the date in the original files and I'm trying that out.

[jaudall]

Now I found this: ../util/buildRMLibFromEMBL.pl RMRBSeqs.embl > RMlib

But is there a certain filename to use? Is the output what I want, or will the embl file be fine?

Answer 2

[Hans]

The workaround, if you have your own repeat library, is to edit Libraries/RepeatMaskerLib.embl. In one of the first lines there is the release date: yyyymmdd. Just change it to what RepeatMasker requires.