Interproscan

Question

[MaxMin]

Hello everyone,

After installing InterProScan and placing Phobius, SignalP, and TMHMM in the folders required by InterPro, the following analyses still appear to be disabled:

Deactivated analyses:
        SignalP_GRAM_NEGATIVE (4.1) : Analysis SignalP_GRAM_NEGATIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
                        TMHMM (2.0c) : Analysis TMHMM is deactivated, because the resources expected at the following paths do not exist: bin/tmhmm/2.0c/decodeanhmm, data/tmhmm/2.0c/TMHMM2.0c.model
                  SignalP_EUK (4.1) : Analysis SignalP_EUK is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp
                      Phobius (1.01) : Analysis Phobius is deactivated, because the resources expected at the following paths do not exist: bin/phobius/1.01/phobius.pl
        SignalP_GRAM_POSITIVE (4.1) : Analysis SignalP_GRAM_POSITIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp

How can I solve this?

[Dunois]

Can you show us the paths where you've placed these files please? (E.g., with ls.)

[MaxMin]

Sure,

interproscan-5.68-100.0/bin/signalp/4.1/signalp

interproscan-5.68-100.0/bin/signalp/4.1/signalp$ ls

conversion_utils  make_output_files.py   predict.py
__init__.py       make_sequence_plot.py  sequential_model.py
__main__.py       model_weights          utils.py

interproscan-5.68-100.0/bin/phobius/1.01

interproscan-5.68-100.0/bin/phobius/1.01$ ls

decodeanhmm        OPSD_SHEEP           phobius.model    phobius.pl  README
decodeanhmm.64bit  phobius_install.txt  phobius.options  Q8TCT8

interproscan-5.68-100.0/bin/tmhmm/2.0c

interproscan-5.68-100.0/bin/tmhmm/2.0c$ ls

decodeanhmm.Linux_i386  decodeanhmm.Linux_ia64    TMHMM2.0.model     tmhmm.ORIG
decodeanhmm.Linux_i486  decodeanhmm.Linux_x86_64  TMHMM2.0.options
decodeanhmm.Linux_i586  tmhmm                     tmhmmformat.pl
decodeanhmm.Linux_i686  TMHMM1.0.model            tmhmm_install.txt

[Dunois]

Thank you.

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signalp:

mv interproscan-5.68-100.0/bin/signalp/4.1/signalp/* interproscan-5.68-100.0/bin/signalp/4.1/

Should fix this one.

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phobius:

I am not sure why this one is malfunctional. Here is what my directory from an older (still functional) version of interproscan looks like for phobius:

interproscan-5.59-91.0/bin/phobius/1.01 > ls
decodeanhmm  decodeanhmm.64bit  LicenseAgreement.txt  OPSD_SHEEP  phobius.model  phobius.options  phobius.pl  Q8TCT8  README

I think it's worth checking phobius_install.txt and the README to see if anything additional has to be done to activate phobius. If you haven't tried executing phobius.pl directly, I'd try this also to see if and also. Executing it with --help specified should produce something like this:

interproscan-5.59-91.0/bin/phobius/1.01 > ./phobius.pl --help
Phobius ver 1.01
(c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

usage: phobius.pl [options] [infile]

  infile            A fasta file with the query protein sequences.
                    If not present input will be read from stdin.

options:
  -h, -help         Show this help message and exit
  -short            Short output. One line per protein.
  -long             Long output. This is the default.
  -raw              decodeanhmm's raw output. This overrides other options.
  -png FILE         If given a posterior label probability plot will be
                    returned in the file FILE in PNG format.
  -gp FILE          Will in combination with the png option write the
                    gnuplot file to produce the plot into the file FILE.
  -plp FILE         If given a posterior label probability values will be 
                    returned in the file FILE in ascii format.

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I cannot advise you regarding tmhmm unfortunately as I do not have it available at hand. But I do remember it was a bit difficult to get running (some paths had to be changed within the main scripts if I recall). But the warnings produced by interproscan simply indicate missing files. You could try copying decodeanhmm.Linux_x86_64 as decodeanhmm and TMHMM2.0.model as TMHMM2.0c.model within the 2.0c subdirectory to see if this fixes the issue already.

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