Phobius error: Could not read provided fasta sequence at phobius.pl line 408

Question

[Elizabeth]

Hello All,

I have been trying to run Phobius to predict TM topology and Signal peptide in my protein sequences. However, the script is just not working. The following command was used:

perl phobius.pl -short proteins.fasta

And, I got the following error:

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.

So, I tried all the solutions mentioned in this post: Phobius:error such as replacing the decodeanhmm with a newer one, renaming the file, editing the script.

However, I still get the same error. Has anyone come across any newer solutions?

Thank you in advance.

[GenoMax]

Is line 408 a blank line in your file by chance?

[Elizabeth]

No. It's part of the script actually. Here is line 408 of the phobius.pl script

line 408  die ("could not read provided fasta sequence") if ($entries_done==0);

[GenoMax]

I see. Is proteins.fasta present in the current directory and readable? Does this make any difference perl phobius.pl -short ./proteins.fasta? What does head -3 proteins.fasta show?

[Elizabeth]

1) Yes, its in the same directory and it's readable. 2) It gives me the same error message. 3) It prints the first 3 lines of my fasta file.

Also, there are no special characters in my fasta file and I have tried running the program on another file, but it still gives me the same error message.

[GenoMax]

If it is any consolation I see the same exact error. This script is from 2004. It appears to be due to an unfortunate combo of perl versions/old libraries.

[GenoMax]

JC : Can you take a look at phobius.pl script to see if it needs to be modified in some way.

[Elizabeth]

Thank you for helping out.

[ido.idobar]

Make sure that your protein fasta doesn't have any * representing stop codons - see this issue in Github.
In my experience, it's either that or the wrong version of decodeanhmm. Can you please provide some details on the system you are using? (operating system, architecture, etc.)