Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-13T14:13:17.787Z
Answers.LastActivityDate: 2019-02-13T14:13:17.787Z
Answers.UserDisplayName: Pawan Verma
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-13T14:02:06.997Z
Comments.Text: Welcome to the site Hilda. I think that the [supported version](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) is now blast+ or something alike. Is there any special reason why you need the legacy 2.2.26? It will get easier to get support and trouble shot the problems if you install the supported version. In addition, it could be that the legacy version does not work with Ubuntu 18.04...
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-14T01:20:11.717Z
Comments.Text: I use tcsh, but I would make a new attempt using bash.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-14T08:29:53.207Z
Comments.Text: I picked the BLAST version based on what seemed to be the most commonly used in forums and similar questions, and that I got the impression that psipred preferes legacy to +. Will definitely try downloading and running BLAST+ instead. Thank you!
Comments.UserDisplayName: Hilda
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-01T02:20:09.740Z
Comments.Text: I'm having the exact same problem. I'm using BLAST+ though and runpsipredplus script. Did you manage to make it run and how did you do it?
Comments.UserDisplayName: Karla Pena Guerra
Tags: <software-installation><psi-blast><makeblastdb>
Title: Error in PSI-BLAST when running psipred locally
ThreadText: # Error in PSI-BLAST when running psipred locally
  
  (Asked by: username_0 on 2019-02-13)
  
  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/username_0/uniref90
  
  # Where the NCBI programs have been installed
  set ncbidir = /home/username_0/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/username_0/uniref90] in search path [/home/username_0/psipred::]
  
  ```
  
  I have also tried setting dbname to home/username_0/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?
  
  **Tags:** software-installation, psi-blast, makeblastdb
  
  > **Comments:**
  > **username_1**: Welcome to the site username_0. I think that the [supported version](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) is now blast+ or something alike. Is there any special reason why you need the legacy 2.2.26? It will get easier to get support and trouble shot the problems if you install the supported version. In addition, it could be that the legacy version does not work with Ubuntu 18.04...  
  > **username_2**: I use tcsh, but I would make a new attempt using bash.  
  > **username_0**: I picked the BLAST version based on what seemed to be the most commonly used in forums and similar questions, and that I got the impression that psipred preferes legacy to +. Will definitely try downloading and running BLAST+ instead. Thank you!  
  > **username_3**: I'm having the exact same problem. I'm using BLAST+ though and runpsipredplus script. Did you manage to make it run and how did you do it?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2019-02-13. Score: 4
  
  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.
  
  
  ---
  
  