text: user4118: I am very new to bioinformatics and Linux and am trying to run psipred locally on Ubuntu 18.04 but cannot get PSI-BLAST to work. I have downloaded BLAST legacy version 2.2.26 and unpacked it, uniref90 database and psipred version 4.01
  I installed psipred according to instructions:
  cd psipred/src
  make
  make install
  
  And this seems to work fine
  I used the following code to create a database, which proceeded without errors:
  makeblastdb -in uniref90.fasta -dbtype prot -out uniref90
  
  In runpsipred I changed the directories:
  # The name of the BLAST data bank
  set dbname = /home/hilda/uniref90
  
  # Where the NCBI programs have been installed
  set ncbidir = /home/hilda/blast/bin
  
  # Where the PSIPRED V4 programs have been installed
  set execdir = ./bin
  
  # Where the PSIPRED V4 data files have been installed
  set datadir = ./data
  
  I then try to run psipred:
  tsch ./runpsipred example/example.fasta
  
  And get the error
  Running PSI-BLAST with sequence example/example.fasta ...
  FATAL: Error whilst running blastpgp - script terminated!
  
  I am not sure how to solve this as I do not understand what is going wrong. As I said I am new to Linux. I use the command tsch to run psipred (otherwise I get the error "command not found"), but not to install the database, could this be a problem? Or have I missed something in the setup process? Running psipred does create a copy of the example.fasta in the psipred folder named psitmp4286007f010.fasta, but that is all that seems to happen. 
  I would greatly appreciate any suggestions on how to make it work!
  Edit:
  I tried to run with BLAST+ (which seemed to work without tsch) and get the following error:
  BLAST Database error: No alias or index file found for protein database [/home/hilda/uniref90] in search path [/home/hilda/psipred::]
  
  I have also tried setting dbname to home/hilda/uniref90/uniref90 and got the same results. there is a uniref90.pal file in the uniref90 directory, which I understand is the alias file? Other forum answers seem to use pfilt to index (?) the database, but there is no pfilt in my psipred directory. Any ideas how to fix the problem?
  
  user4121: This error could be due to the fact that you are using legacy blast, have you tried using BLAST+ instead?
  If you wish to use PSIPRED with BLAST+, then use the runpsipredplus script
  here, rather than the normal runpsipred script.
  
original_text: 4118: <p>I am very new to bioinformatics and Linux and am trying to run psipred locally on Ubuntu 18.04 but cannot get PSI-BLAST to work. I have downloaded BLAST legacy version 2.2.26 and unpacked it, uniref90 database and psipred version 4.01</p>
  
  <p>I installed psipred according to instructions:</p>
  
  <pre><code>cd psipred/src
  make
  make install
  </code></pre>
  
  <p>And this seems to work fine</p>
  
  <p>I used the following code to create a database, which proceeded without errors:</p>
  
  <pre><code>makeblastdb -in uniref90.fasta -dbtype prot -out uniref90
  </code></pre>
  
  <p>In runpsipred I changed the directories:</p>
  
  <pre><code># The name of the BLAST data bank
  set dbname = /home/hilda/uniref90
  
  # Where the NCBI programs have been installed
  set ncbidir = /home/hilda/blast/bin
  
  # Where the PSIPRED V4 programs have been installed
  set execdir = ./bin
  
  # Where the PSIPRED V4 data files have been installed
  set datadir = ./data
  </code></pre>
  
  <p>I then try to run psipred:</p>
  
  <pre><code>tsch ./runpsipred example/example.fasta
  </code></pre>
  
  <p>And get the error</p>
  
  <pre><code>Running PSI-BLAST with sequence example/example.fasta ...
  FATAL: Error whilst running blastpgp - script terminated!
  </code></pre>
  
  <p>I am not sure how to solve this as I do not understand what is going wrong. As I said I am new to Linux. I use the command tsch to run psipred (otherwise I get the error "command not found"), but not to install the database, could this be a problem? Or have I missed something in the setup process? Running psipred does create a copy of the example.fasta in the psipred folder named psitmp4286007f010.fasta, but that is all that seems to happen. </p>
  
  <p>I would greatly appreciate any suggestions on how to make it work!</p>
  
  <p>Edit:
  I tried to run with BLAST+ (which seemed to work without tsch) and get the following error:</p>
  
  <pre><code>BLAST Database error: No alias or index file found for protein database [/home/hilda/uniref90] in search path [/home/hilda/psipred::]
  </code></pre>
  
  <p>I have also tried setting dbname to home/hilda/uniref90/uniref90 and got the same results. there is a uniref90.pal file in the uniref90 directory, which I understand is the alias file? Other forum answers seem to use pfilt to index (?) the database, but there is no pfilt in my psipred directory. Any ideas how to fix the problem?</p>
   4121: <p>This error could be due to the fact that you are using legacy blast, have you tried using BLAST+ instead?
  If you wish to use PSIPRED with BLAST+, then use the runpsipredplus script
  here, rather than the normal runpsipred script.</p>
  