Problems with using Phobius

Question

[logleg92029]

Hello everyone,

I refer to the link https://www.protocols.io/view/identification-of-proteins-containing-transmembran-pdwdi7e

I have followed the method listed here to identify Transmembrane proteins and downloaded the relevant programs. For example I have a file examplefasta.fna and wish to run it through Phobius:

Upon running the script (given on the link above) in Phobius to detect TM proteins:

phobius.pl -short examplefasta.fna \
  | tail -n+2 | tr -s ' ' | tr ' ' '\t' \
  | awk -F '\t' '$2 > 0' > examplefastatm.tsv

I get the following messages:

Use of uninitialized value $predstr in concatenation (.) or string at /home/logleg92029/bin/phobius101_linux/tmp/tmpFQ5Tig/phobius/phobius.pl line 248, <SOUT> line 10.

which repeats itself over several instances. I have followed the solutions given in Has anyone run Phobius locally? Error - could not read provided fasta sequences (for a different error message I was getting), and this was fixed, but I still have the above issue.

I have looked at the variable $predstr in phobius.pl but I am unsure if it should be fixed or set to a specific value (i am new to scripting but trying to learn as much as possible)

Please advise me on a solution Thank you.

Answer 1

[Marina]

In case anyone else runs into this problem: I was getting the same messages when running Phobius 1.01 locally, but the program was still running and producing the results that I was expecting. I set $predstr=""; in phobius.pl before entering the loop where $predstr is updated and that seemed to remove the warnings in my case.