Error: it does not contain a 'Libraries' or 'Matrices' subdirectory

[kazuaki0816]

What do you want to know? I'm using RepeatMasker version 4.1.2-p1.

I get an error when I run the following command: /home/user/local/tool/RepeatMasker/RepeatMasker -lib /home/user/local/tool/RepeatModeler/db/species_final-families.fa /home/user/local/sample_genome.fasta -pa 45 -xsmall -poly -html -ace -gff -excln &> /home/user/local/repeatmasker.log &

The error is: The assumed RepeatMasker installation directory /home/user/local/tool/RepeatMasker does not appear to be correct. E.g it does not contain a 'Libraries' or 'Matrices' subdirectory. This can occur if hard links are used to invoke this script. RepeatMasker version 4.1.2-p1

I have confirmed that these two subdirectories, 'Libraries' and 'Matrices', exist in the RepeatMasker directory. I performed RepeatModeler according to the following page (https://www.repeatmasker.org/RepeatModeler/) and use the output data as a lib file. I use RepeatMasker by compiling the source code from Github.

I want to solve this trouble. I would be grateful if you could help me.

• Have you installed RepBase RepeatMasker Edition for RepeatMasker? Yes

[jebrosen]

I use RepeatMasker by compiling the source code from Github.

Please try this again with a full release build (as mentioned in the README):

IMPORTANT: The github 'master' branch only contains the source code files for the latest release of RepeatMasker. A complete distribution including the source files, a copy of the Dfam database, and the required taxonomy data file may be found at the RepeatMasker website: http://www.repeatmasker.org/RMDownload.html

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The error is: The assumed RepeatMasker installation directory /home/user/local/tool/RepeatMasker does not appear to be correct. E.g it does not contain a 'Libraries' or 'Matrices' subdirectory. This can occur if hard links are used to invoke this script.

Additionally, did you perhaps not run configure? configure must be run to initialize some paths, including the Libraries/ directory.

[toddajohnson]

Just had the same problem. As mentioned in the error, there actually was a problem with "hard links". The path under RepeatMasker/Libraries for RepeatMaskerLib.h5 was a symbolic link pointing to RepeatMasker/Libraries/Dfam.h5 but included a full physical path that has changed since the server underwent maintenance; the underlying physical volumes holding our user directories changed, so the physical path was no longer valid.