Answers.Body: <p>Thanks, I did this but got this erro:</p>
  
  <pre><code>blastpgp -a 12 -b 0 -j 3 -h 0.001 -d c600m2-tail-before-lysin-sequence.a3m -i c600m2-tail-before-lysin-sequence.temp.fasta
  [blastpgp] WARNING: Unable to open BLOSUM62
  [blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
  [blastpgp] WARNING: SetUpBlastSearch failed.
  BLASTP 2.2.26 [Sep-21-2011]
  
  
  Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
  Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
  "Gapped BLAST and PSI-BLAST: a new generation of protein database search
  programs",  Nucleic Acids Res. 25:3389-3402.
  
  
  Reference for compositional score matrix adjustment: Altschul, Stephen F., 
  John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
  Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
  using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
  
  
  Reference for composition-based statistics starting in round 2:
  Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
  Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
  Eugene V. Koonin, and Stephen F. Altschul (2001), 
  "Improving the accuracy of PSI-BLAST protein database searches with 
  composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.
  
  Query= C600M2_00100 tail protein [Salmonella phage BPS17S6]
           (377 letters)
  
  Database: c600m2-tail-before-lysin-sequence.a3m 
             46,978 sequences; 11,323,713 total letters
  
  SearchingSegmentation fault (core dumped)
  </code></pre>
  
  <p>Could you please let me know how this could be solved? Thanks</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T15:27:27.530Z
Answers.Text: Ok, I got it resolved by changing the correct blastpgp (legacy blast) executable. Thanks!
Answers.UserDisplayName: DanielSebas
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T12:37:33.550Z
Answers.LastActivityDate: 2019-09-10T12:37:33.550Z
Answers.UserDisplayName: DanielSebas
Answers.Body: <p>The comment by Devon Ryan is correct - looks like your <code>blastpgp</code> command is not working properly. For a protein of that length it's more likely to be a problem with the BLAST executable running on your system than a memory issue.</p>
  
  <p>Try running the <code>blastpgp</code> command (<a href="https://github.com/psipred/DMPfold/blob/master/bin/runpsipredandsolvwithdb#L26" rel="nofollow noreferrer">https://github.com/psipred/DMPfold/blob/master/bin/runpsipredandsolvwithdb#L26</a>) on its own and see what happens:</p>
  
  <pre><code>~/path/to/blastpgp -a 12 -b 0 -j 3 -h 0.001 -d yourfile.a3m -i yourfile.fasta
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T11:37:43.657Z
Answers.LastActivityDate: 2019-09-10T11:37:43.657Z
Answers.UserDisplayName: jgreener
Body: <p>I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between:</p>
  
  <pre><code>Running PSIPRED &amp; SOLVPRED
  Running PSI-BLAST with sequence c600m2-tail-before-lysin-sequence.temp.fasta ...
  Segmentation fault (core dumped)
  [blastpgp] WARNING: Unable to open BLOSUM62
  [blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
  [blastpgp] WARNING: SetUpBlastSearch failed.
  BLASTP 2.2.17 [Aug-26-2007]
  
  
  Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
  Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
  "Gapped BLAST and PSI-BLAST: a new generation of protein database search
  programs",  Nucleic Acids Res. 25:3389-3402.
  
  
  Reference for composition-based statistics:
  Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
  Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
  Eugene V. Koonin, and Stephen F. Altschul (2001), 
  "Improving the accuracy of PSI-BLAST protein database searches with 
  composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.
  
  Query= C600M2_00100 tail protein [Salmonella phage BPS17S6]
           (377 letters)
  
  Database: c600m2-tail-before-lysin-sequence.a3m 
             46,978 sequences; 11,323,713 total letters
  
  SearchingFATAL: Error whilst running blastpgp - script terminated!
  Running PSICOV
  Running FreeContact
  Running CCMpred
   _____ _____ _____               _ 
  |     |     |     |___ ___ ___ _| |
  |   --|   --| | | | . |  _| -_| . |
  |_____|_____|_|_|_|  _|_| |___|___|
                    |_|              
  
  using CPU (10 thread(s))
  
  Reweighted 30404 sequences with threshold 0.8 to Beff=22917.9 weight mean=0.753779, min=0.0232558, max=1
  
  Will optimize 62686429 32-bit variables
  
  iter    eval    f(x)        ║x║         ║g║         step
  1       1       1.50338e+07 152357      3.021629e+11    1.55e-06
  2       1       1.47369e+07 152356      2.1447226e+11   1.18e-06
  3       1       1.44292e+07 152355      1.4646483e+11   1.22e-06
  4       1       1.41268e+07 152353      1.0388224e+11   1.5e-06
  5       1       1.38295e+07 152358      7.337667e+10    1.92e-06
  </code></pre>
  
  <p>Can you please let me know if I need to rerun seq2maps.csh because of this error? And, how this error can be solved? Thank you!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-10T10:11:55.937Z
Comments.Text: The `blastpgp` command threw a segfault, so either it has a bug or you ran out of memory. Yes, you need to rerun things, but do so on a different computer (with more memory) or using a different blast installation.
Comments.UserDisplayName: Devon Ryan
Tags: <protein-structure>
Title: DMPfold error while running protein structure prediction
ThreadText: # DMPfold error while running protein structure prediction
  
  (Asked by: username_0 on 2019-09-10)
  
  I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between:
  
  ```
  Running PSIPRED & SOLVPRED
  Running PSI-BLAST with sequence c600m2-tail-before-lysin-sequence.temp.fasta ...
  Segmentation fault (core dumped)
  [blastpgp] WARNING: Unable to open BLOSUM62
  [blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
  [blastpgp] WARNING: SetUpBlastSearch failed.
  BLASTP 2.2.17 [Aug-26-2007]
  
  Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
  Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
  "Gapped BLAST and PSI-BLAST: a new generation of protein database search
  programs",  Nucleic Acids Res. 25:3389-3402.
  
  Reference for composition-based statistics:
  Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
  Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
  Eugene V. Koonin, and Stephen F. Altschul (2001), 
  "Improving the accuracy of PSI-BLAST protein database searches with 
  composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.
  
  Query= C600M2_00100 tail protein [Salmonella phage BPS17S6]
           (377 letters)
  
  Database: c600m2-tail-before-lysin-sequence.a3m 
             46,978 sequences; 11,323,713 total letters
  
  SearchingFATAL: Error whilst running blastpgp - script terminated!
  Running PSICOV
  Running FreeContact
  Running CCMpred
   _____ _____ _____               _ 
  |     |     |     |___ ___ ___ _| |
  |   --|   --| | | | . |  _| -_| . |
  |_____|_____|_|_|_|  _|_| |___|___|
                    |_|              
  
  using CPU (10 thread(s))
  
  Reweighted 30404 sequences with threshold 0.8 to Beff=22917.9 weight mean=0.753779, min=0.0232558, max=1
  
  Will optimize 62686429 32-bit variables
  
  iter    eval    f(x)        ║x║         ║g║         step
  1       1       1.50338e+07 152357      3.021629e+11    1.55e-06
  2       1       1.47369e+07 152356      2.1447226e+11   1.18e-06
  3       1       1.44292e+07 152355      1.4646483e+11   1.22e-06
  4       1       1.41268e+07 152353      1.0388224e+11   1.5e-06
  5       1       1.38295e+07 152358      7.337667e+10    1.92e-06
  
  ```
  
  Can you please let me know if I need to rerun seq2maps.csh because of this error? And, how this error can be solved? Thank you!
  
  **Tags:** protein-structure
  
  > **Comments:**
  > **username_1**: The `blastpgp` command threw a segfault, so either it has a bug or you ran out of memory. Yes, you need to rerun things, but do so on a different computer (with more memory) or using a different blast installation.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2019-09-10. Score: 1
  
  The comment by username_1 username_1 is correct - looks like your `blastpgp` command is not working properly. For a protein of that length it's more likely to be a problem with the BLAST executable running on your system than a memory issue.
  
  Try running the `blastpgp` command (<https://github.com/psipred/DMPfold/blob/master/bin/runpsipredandsolvwithdb#L26>) on its own and see what happens:
  
  ```
  ~/path/to/blastpgp -a 12 -b 0 -j 3 -h 0.001 -d yourfile.a3m -i yourfile.fasta
  
  ```
  
  
  ---
  
  ### Answer by username_0 on 2019-09-10. Score: 0
  
  Thanks, I did this but got this erro:
  
  ```
  blastpgp -a 12 -b 0 -j 3 -h 0.001 -d c600m2-tail-before-lysin-sequence.a3m -i c600m2-tail-before-lysin-sequence.temp.fasta
  [blastpgp] WARNING: Unable to open BLOSUM62
  [blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
  [blastpgp] WARNING: SetUpBlastSearch failed.
  BLASTP 2.2.26 [Sep-21-2011]
  
  Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
  Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
  "Gapped BLAST and PSI-BLAST: a new generation of protein database search
  programs",  Nucleic Acids Res. 25:3389-3402.
  
  Reference for compositional score matrix adjustment: Altschul, Stephen F., 
  John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
  Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
  using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
  
  Reference for composition-based statistics starting in round 2:
  Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
  Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
  Eugene V. Koonin, and Stephen F. Altschul (2001), 
  "Improving the accuracy of PSI-BLAST protein database searches with 
  composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.
  
  Query= C600M2_00100 tail protein [Salmonella phage BPS17S6]
           (377 letters)
  
  Database: c600m2-tail-before-lysin-sequence.a3m 
             46,978 sequences; 11,323,713 total letters
  
  SearchingSegmentation fault (core dumped)
  
  ```
  
  Could you please let me know how this could be solved? Thanks
  
  > **Comments:**
  > **username_0**: Ok, I got it resolved by changing the correct blastpgp (legacy blast) executable. Thanks!  
  
  ---
  
  