Phobius error: Could not read provided fasta sequence at phobius.pl line 408
0
0
Entering edit mode
12 weeks ago
Elizabeth ▴ 30

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.

Phobius • 614 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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);
ADD REPLY
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Thank you for helping out.

ADD REPLY
0
Entering edit mode

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.)

ADD REPLY

Login before adding your answer.

Traffic: 2118 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6