I am currently trying to run Phobius (http://phobius.sbc.su.se/data.html) in LInux to predict signal peptides in some proteins. I am not sure if anyone has run this recently, but please help me if you have!
After typing in the absolute path to the directory in phobius.pl:
my $PHOBIUS_DIR = "/full/path/to/phobius";
In that directory, I typed in the command below. test.fasta existed in the same folder. Then, it returned
perl phobius.pl -short test.fasta
Phobius ver 1.01
(c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer
SEQENCE ID TM SP PREDICTION
Could not read provided fasta sequence at phobius.pl line 408.
Test.fasta looks like just usual a fasta file with >seq1 \n sequences