RepeatMasker help needed

[Olalla]

Hello all

I have downloaded and installed RepeatMasker in my computer. When running the perl ./configure, all went fine, but at the end, after setting the searching engine (rmblastn), this is what I got:

-- Setting perl interpreter...
Can't remove RepeatMasker: permission denied, skipping file.
Can't remove DateRepeats: Permiso denegado, skipping file.
Can't remove ProcessRepeats: Permiso denegado, skipping file.
Can't remove RepeatProteinMask: Permiso denegado, skipping file.
Can't remove DupMasker: Permiso denegado, skipping file.
Can't remove util/queryRepeatDatabase.pl: Permiso denegado, skipping file.
Can't remove util/queryTaxonomyDatabase.pl: Permiso denegado, skipping file.
Can't remove util/rmOutToGFF3.pl: Permiso denegado, skipping file.
Can't remove util/rmToUCSCTables.pl: Permiso denegado, skipping file.

However, the program seems to have been succesfully installed:


Congratulations! RepeatMasker is now ready to use.
The program is installed with a full version of the repeat library:
DFAM Library Version = Dfam_1.2
RMLibrary Version = 20140131
Repbase Version = 20140131
Further documentation on the program may be found here:
/home/RepeatMasker/repeatmasker.help

So according to this, the program is installed and ready to use. I do have a fasta file of contigs (low coverage genomic data) on which I do want to run RepeatMasker. The file is located in the RepeatMasker folder (which I think is mandatory?), however, when I try to run the program as follows:

RepeatMasker Mnais-SSPACE-scaffolds.k49.ncbi.fa

I get the following error: RepeatMasker: order not found


Any idea on what is going on, and how I can solve this problem would be more than welcome

Thanks a lot in advance

Olalla

[SES]

The issue is that you need to specify the path to the program, so the command would be:

./RepeatMasker Mnais-SSPACE-scaffolds.k49.ncbi.fa

Also, you don't need to run the program from within that repeatmasker directory, but you will need to specify the path to the program (or extend your PATH variable so the program can be found).

[Olalla]

Hello

Thanks for your reply, the problem is solved now. THis was an issue with permissions of the folder. Now running correctly

Olalla

[SES]

Oh yeah, permissions will cause the shell to say the program couldn't be found also. Anyway, glad you got it solved!