This fixed it for me -
./decodeanhmm
would result in an error:
-bash: ./decodeanhmm: No such file or directory
(how is that even possible? the file is right there!), so I downloaded this copy: https://github.com/chefnb/ParseTargs/blob/master/tmhmm-2.0c/bin/decodeanhmm
and tried to run phobius.pl and got output immediately, instead of the above 'could not read provided fasta file'
In my case this was causing problems in the RGaugury pipeline, where the files with RLK and RLP candidate genes were empty because of phobius not working properly.
Edit: I now figured out what the No such file or directory error means. If you use the strings tool on the decodeanhmm binary that comes with phobius, you'll see this file pop up:
/lib/ld-linux.so.2
On my system that file doesn't exist, which causes the error. The decodeanhmm in the ParseTargs package doesn't have that string in its header, so it doesn't look for that file. The decodeanhmm.64bit file that comes with phobius also doesn't have that file, maybe renaming decodeanhmm.64bit to decodeanhmm (overwriting the 'original') fixes this problem too?
I met the same problem, any solution so far?
In my case, Duan's solution worked for me. I copied decodeanhmm.Linux_i686 from tmhmm-2.0c/bin to the Phobius folder as decodeanhmm.
You shouldn't need to alter the line:
The FindBin module function is to locates the full path to the script bin directory, to allow the use of paths relative to the bin directory, so there should be no need to hard-code paths into the script.