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.
