issue with psipred
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Entering edit mode
16 months ago

I am trying to run pgenthreader.sh script, the result is :

Finished 3 iterations PSI-BLAST
usage : psipred weight-file seq-file
usage : psipass2 weight-file seq-file DCA DCB
PSIPRED failed ... exiting early

(It is creating the sequence.pgen.ss file but its blank) so, I tried to run psipred command separately :

/media/kakarot/ppi/psipred/bin$ psipred /media/kakarot/ppi/genthreader/sequence.iter3.mtx /media/kakarot/ppi/psipred/data/weights.dat /media/kakarot/ppi/psipred/data/weights.dat2 /media/kakarot/ppi/psipred/data/weights.dat3 > /media/kakarot/ppi/genthreader/sequence.pgen.ss

But i am getting : psipred: command not found

sequence software error • 381 views
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Thank u so much for your reply. I have typed the correct path where the program is exist. I think the problem is with psipred. I have read the README file... it ask to use the tcsh shell to execute the psipred command. As I am using Linux (Ubuntu), It requires csh instead of tcsh. I installed and changed the shell also ...still it says psipred command not found...

$ csh
% cd /media/kakarot/ppi/psipred/
% cd src
% make
make: Nothing to be done for 'all'.
% make install
/bin/cp psipred psipass2 chkparse seq2mtx ../bin
% cd ..
% cd bin
% psipred /media/kakarot/ppi/genthreader/sequence.iter3.mtx /media/kakarot/ppi/psipred/data/weights.dat /media/kakarot/ppi/psipred/data/weights.dat2 /media/kakarot/ppi/psipred/data/weights.dat3 > /media/kakarot/ppi/genthreader/sequence.pgen.ss
psipred: Command not found.
% psipred /media/kakarot/ppi/genthreader/sequence.iter3.mtx /media/kakarot/ppi/psipred/data/weights.dat /media/kakarot/ppi/psipred/data/weights.dat2 /media/kakarot/ppi/psipred/data/weights.dat3 > /media/kakarot/ppi/genthreader/sequence.pgen.ss
psipred: Command not found.
%
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Please use ADD COMMENT/ADD REPLY when responding to existing answers/comments to keep threads logically organized.

Ubuntu does not require csh. Have you managed to compile psipred? What do you get when you do ls -lh /media/kakarot/ppi/psipred//bin/psipred? If psipred executable is there (you see a listing) then you just need to add /media/kakarot/ppi/psipred/bin to your $PATH. Details on how to do this for different shells are here.

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Entering edit mode
16 months ago
Mensur Dlakic ★ 11k

But i am getting : psipred: command not found

One of the classic issues in Linux: the system can't see the command the user is trying to execute. That is either because the command doesn't exist (mistyped the name or actually never compiled/installed) or because it is somewhere where the system is not looking. Can't tell from you description which one is the case.

If the program exists, it needs to be placed in the PATH, or the whole program location needs to be typed (something like /directory/that/contains/psipred). If you don't know what this means, let me know and I can explain further.

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