rsem-calculate-expression searches for reference genome in the directory parent to the path directory.
E.g. you specify reference as "root/a/b/c/ref" - the program will look for reference files in root/a/b/c and breaks and sends an error message.
I have fixed it by changing line 263 in rsem-calculate-expression file found in /lib/ (I use Conda environment) from my "$star_genome_path = dirname($refName);" to "my $star_genome_path = $refName;". It seems like the function dirname looks for a parent directory (like when you look for one of a file). However, the user specified input to --genomeDir for STAR is always a directory, not a file, a does not require looking for its parent directory
rsem-calculate-expression searches for reference genome in the directory parent to the path directory.
E.g. you specify reference as "root/a/b/c/ref" - the program will look for reference files in root/a/b/c and breaks and sends an error message.
I have fixed it by changing line 263 in rsem-calculate-expression file found in /lib/ (I use Conda environment) from my "$star_genome_path = dirname($refName);" to "my $star_genome_path = $refName;". It seems like the function dirname looks for a parent directory (like when you look for one of a file). However, the user specified input to --genomeDir for STAR is always a directory, not a file, a does not require looking for its parent directory