search

rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
Other
214 stars 48 forks source link

error: The assumed RepeatMasker installation directory does not appear to be correct. #218

Open DavidCamAr opened 1 year ago

DavidCamAr commented 1 year ago

Hi, I installed and set up RepeatMasker following command from the RepeatMasker Download (http://www.repeatmasker.org/RepeatMasker/)

When I run the following command: $ RepeatMasker -s -a -species 'homo_sapiens' ../../007-bam2fasta/results/SRR6941195.filtered-sam.fa

I get this error message like the other users: RepeatMasker version 4.1.4 The assumed RepeatMasker installation directory /datos/bin/RepeatMasker/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.

But, the 'Libraries' and 'Matrices' subdirectories exist in the RepeatMasker directory $/datos/bin/RepeatMasker/RepeatMasker/Libraries $/datos/bin/RepeatMasker/RepeatMasker/Matrices

Am I doing something wrong? is there a problem with hard links?

rmhubley commented 11 months ago

Ah...I think you identified the problem. I suspect that the test for the existence of those directories in perl doesn't like the use of hard links. Have you tried a symbolic link instead?