I am trying to run the Prokka annotation tool on my linux machine and have installed Barrnap and added it to $PATH and given the folder chmod 777 permission. However, when running Prokka, it gives the line
Could not parse version from 'sh: 1: barrnap: Permission denied'.
Running Barrnap solely through the command line with a valid input works fine but does not seem to work when another script calls barrnap. I have tried checking path variables and giving max permissions to barrnap and Prokka but it does not seem to change this error. Here is the full log file:
[15:01:28] This is prokka 1.14.6 [15:01:28] Written by Torsten Seemann <email@example.com> [15:01:28] Homepage is https://github.com/tseemann/prokka [15:01:28] Local time is Thu Feb 23 15:01:28 2023 [15:01:28] You are saurab [15:01:28] Operating system is linux [15:01:28] You have BioPerl 1.7.8 [15:01:28] System has 16 cores. [15:01:28] Will use maximum of 8 cores. [15:01:28] Annotating as >>> Bacteria <<< [15:01:28] Generating locus_tag from 'jobs/NC_004556.faa' contents. [15:01:28] Setting --locustag ECJHPMJE from MD5 ec31963ed5d3d76e28501fa7e45ca273 [15:01:28] Creating new output folder: PROKKA_02232023 [15:01:28] Running: mkdir -p PROKKA_02232023 [15:01:28] Using filename prefix: PROKKA_02232023.XXX [15:01:28] Setting HMMER_NCPU=1 [15:01:28] Writing log to: PROKKA_02232023/PROKKA_02232023.log [15:01:28] Command: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/prokka jobs/NC_004556.faa [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/../binaries/linux [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin/../binaries/linux/../common [15:01:28] Appending to PATH: /home/saurab/BIOIN/basys2-app/sub_programs/prokka/bin [15:01:28] Looking for 'aragorn' - found /home/saurab/BIOIN/phastest-app/sub_programs/aragorn [15:01:28] Determined aragorn version is 001002 from 'ARAGORN v1.2 Dean Laslett' [15:01:28] Looking for 'barrnap' - found /home/saurab/BIOIN/phastest-app/sub_programs/barrnap [15:01:28] Coult not parse version from 'sh: 1: barrnap: Permission denied'
ls -l /home/saurab/BIOIN/phastest-app/sub_programs/barrnap. You say you set the directory to 777 but what about the actual script/executable? $\endgroup$