error "RepeatMasker installation directory does not appear to be correct"

[jebrosen]

Hi!! I am implementing RepeatMasker4.1.1 While using the tool, I came across an error

Command: ./RepeatMasker -species fungi /home/guest1/assembly.fasta -dir /home/guest1/maker/RM_output

Output: The assumed RepeatMasker installation directory /home/guest1/maker/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.

Kindly help. I shall be highly obliged.

Originally posted by @aditi17142 in https://github.com/rmhubley/RepeatMasker/issues/19#issuecomment-811821864

[jebrosen]

@aditi17142

The assumed RepeatMasker installation directory /home/guest1/maker/RepeatMasker does not appear to be correct

Did you install RepeatMasker in the directory named /home/guest1/maker/RepeatMasker, or was RepeatMasker installed automatically as part of the MAKER package? Both the directories /home/guest1/maker/RepeatMasker/Libraries and /home/guest1/maker/RepeatMasker/Matrices should exist, unless RepeatMasker was specifically configured with a different Libraries directory.

./RepeatMasker -species fungi

Please also note that RepeatMasker's default library (the curated families in Dfam) contains no fungi-specific entries. At this time, you will get more useful results if you install RepBase RepeatMasker Edition (requires a license), or another library of fungal TEs (either curated or de novo, depending on how you are using the output).

[aditi17142]

Thank you for replying @jebrosen I would like to mention that both the folders Libraries and Matrices are present within the folder where RepeatMasker is installed. Still the error is showing up.

[aditi17142]

I have been now trying to install RepeatMasker v4.1.2 on another system In order to download its dependency TRF, I downloaded it But while installing, I have encountered an error

Command: make Output: CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash /home/Desktop/GenomeAnnotation/RepeatMasker/TRF/missing aclocal-1.16 /home/Desktop/GenomeAnnotation/RepeatMasker/TRF/missing: line 81: aclocal-1.16: command not found WARNING: 'aclocal-1.16' is missing on your system. You should only need it if you modified 'acinclude.m4' or 'configure.ac' or m4 files included by 'configure.ac'. The 'aclocal' program is part of the GNU Automake package: https://www.gnu.org/software/automake It also requires GNU Autoconf, GNU m4 and Perl in order to run: https://www.gnu.org/software/autoconf https://www.gnu.org/software/m4/ https://www.perl.org/ Makefile:375: recipe for target '../aclocal.m4' failed make: *** [../aclocal.m4] Error 127

I checked this module. And its already present. Kindly guide.

[jebrosen]

I would like to mention that both the folders Libraries and Matrices are present within the folder where RepeatMasker is installed. Still the error is showing up.

What is the value of the LIBDIR configuration in /home/guest1/maker/RepeatMasker/RepeatMaskerConfig.pm? That directory should normally be /home/guest1/maker/RepeatMasker/Libraries. If both the Libraries and Matrices directories exist, there may be a different issue such as file permissions.

Here's another possibility - what does realpath ./RepeatMasker say if you run it where you ran ./RepeatMasker?

I have been now trying to install RepeatMasker v4.1.2 on another system In order to download its dependency TRF, I downloaded it But while installing, I have encountered an error

TRF is also available as a binary for most platforms (e.g. on Linux x86_64, trf409.linux64 from https://github.com/Benson-Genomics-Lab/TRF/releases/tag/v4.09.1) so you probably don't actually need to compile it yourself.

Command: make (error message...) I checked this module. And its already present.

We will need much more detail than this if you do need to compile TRF yourself and have further issues. e.g. What commands did you run before make, and were there any errors? What module did you check? And how did you check it (e.g. which command or file?)