Both Signalp 4.1 and TMHMM 2 do not work

[rforster1]

I followed your installation tutorial on gitbucket and the directions in the TMHMM 2/Signalp 4.1 readme files. So that includes editing the path of perl in the executable perl scripts.

$which perl
/home/rphorsterphages_gmail_com/miniconda3/envs/inovirus_detector/bin/perl

$perl -v
This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

When working with the Example data files, I initially ran:
./Identify_candidate_fragments_from_gbk.pl

I specified paths to the installation of pfam-A, Signalp 4.1 and TMHMM 2. I never got the gff output.

I attempted to run:
./Predict_inovirus_coat_proteins.pl -f ~/Inovirus_detector/Example_files/2731957639/2731957639_129103.assembled_frag_Ga0128599_102362_prots.faa -sp /home/rphorsterphages_gmail_com/signalp-4.1/ -th /home/rphorsterphages_gmail_com/tmhmm-2.0c/bin/

The output I recieved was :
Error_output_ino_coat.txt

I decided to test the stand alone installations of TMHMM2 and got segmentation error after that.

I have reached out to the developers of these scripts and I am awaiting a reply. I wasn't sure if you have any input, but any thoughts?

Thank you for your time!

[simroux]

Hi ! I think you are actually pretty close: the paths provided as arguments to "./Identify_candidate_fragments_from_gbk.pl" must be the paths to the signalp and tmhmm executables (when using SignalP 4), not the to the folders. Based on your current paths, these should look something like: "-sp /home/rphorsterphages_gmail_com/signalp-4.1/signalp -th /home/rphorsterphages_gmail_com/tmhmm-2.0c/bin/tmhmm"

[rforster1]

Hey! thanks for the quick reply. I made the suggested fixes. This only fixed signalp. However I'm still getting segmentation error with using tmhmm and not getting the expected output with the example files. Here is the output:
Segmentation_error_output.txt

[simroux]

Hmm not sure what happens with the segmentation fault here, unfortunately it seems like this happens during TMHMM execution, and I have never seen this, so this is probably best answered by the TMHMM developers ?