Question: Has anyone run Phobius locally? Error - could not read provided fasta sequences
0
gravatar for s.kyungyong64
21 months ago by
Berkeley, USA
s.kyungyong6410 wrote:

Hi,

I am currently trying to run Phobius (http://phobius.sbc.su.se/data.html) in LInux to predict signal peptides in some proteins. I am not sure if anyone has run this recently, but please help me if you have!

After typing in the absolute path to the directory in phobius.pl:


my $PHOBIUS_DIR = "/full/path/to/phobius";


In that directory, I typed in the command below. test.fasta existed in the same folder. Then, it returned


perl phobius.pl -short test.fasta

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.

Test.fasta looks like just usual a fasta file with >seq1 \n sequences

sequence • 1.1k views
ADD COMMENTlink modified 4 months ago by h.mon21k • written 21 months ago by s.kyungyong6410

I met the same problem, any solution so far?

ADD REPLYlink written 20 months ago by Guangyou Duan20

In my case, Duan's solution worked for me. I copied decodeanhmm.Linux_i686 from tmhmm-2.0c/bin to the Phobius folder as decodeanhmm.

ADD REPLYlink written 19 months ago by yongjoon0

You shouldn't need to alter the line:

my $PHOBIUS_DIR = "$FindBin::RealBin";

The FindBin module function is to locates the full path to the script bin directory, to allow the use of paths relative to the bin directory, so there should be no need to hard-code paths into the script.

ADD REPLYlink written 4 months ago by h.mon21k
2
gravatar for Guangyou Duan
20 months ago by
China/Jinan
Guangyou Duan20 wrote:

It could be the problem of decodeanhmm, in my case I copy a new decodeanhmm from the installation directory of tmhmm-2.0c and it works.

ADD COMMENTlink written 20 months ago by Guangyou Duan20
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