make_fragments.pl error – Rosetta Commons

This topic has 2 replies, 2 voices, and was last updated 4 years, 4 months ago by Anonymous.

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- August 31, 2020 at 11:39 am #3560
  Anonymous
  Hello,
  
  I am trying to run make_fragments.pl but I get this error:
  
  FILENAME: lig_0.fasta
  
  Sequence: DDYLWGLEAGEGISDLFD
  
  Running sparks for phi, psi, and solvent accessibility predictions
  
  running psiblast for sequence: lig_0.fasta
  
  [blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
  
  At line 239 of file phipsi_ss0.f (unit = 77, file = ‘/mnt/data/yalmeida/Softwares/rosetta_src_2020.08.61146_bundle/tools/fragment_tools/sparks-x/SPINE-X/weights/ss0/av1/fort’)
  
  Fortran runtime error: End of file
  
  Aborting: Can’t run first SS0 predictor
  
  Error in file: lig_0.fasta.phipsi
  
  Traceback (most recent call last):
  
  File “/mnt/data/yalmeida/Softwares/rosetta_src_2020.08.61146_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 255, in run1
  
  buildinp(fphipsiss, fmat, finp)
  
  File “/mnt/data/yalmeida/Softwares/rosetta_src_2020.08.61146_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 238, in buildinp
  
  seq1, ssec1, phipsi1, Fphipsi = rdphipsi(fphipsiss)
  
  File “/mnt/data/yalmeida/Softwares/rosetta_src_2020.08.61146_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 9, in rdphipsi
  
  for line in file(fn):
  
  IOError: [Errno 2] No such file or directory: ‘lig_0.fasta.phipsi’
  
  sparks path length > 100 characters, which may cause internal errors. Try moving to a shorter path prefix.
  
  sparks failed!
  
  The install_dependiencies.pl script ran OK with the uniprot50 database (I got the same problem as in https://www.rosettacommons.org/node/10770).
  
  Any thoughts?
  
  Regards and thanks in advance.
- August 31, 2020 at 6:37 pm #15471
  Anonymous
  Hello,
  
  the lines:
```
sparks path length > 100 characters, which may cause internal errors. Try moving to a shorter path prefix.

sparks failed!
```
  means that some dependency requires your path length to be shorter than 100 characters (its very sad I know)
  
  so maybe try moving your directory of
  
  /mnt/data/yalmeida/Softwares/rosetta_src_2020.08.61146_bundle
  
  to:
  
  /mnt/data/yalmeida/Softwares/rosetta
  
  maybe that willl give you enough characters for sparksX to work!
  - September 1, 2020 at 8:29 am #15472
    Anonymous
    Hello,
    
    Thank you for your reply. I renamed rosetta_src_2020.08.61146_bundle to Rosetta, moved my input .fasta file to tools/fragment_tools, and made a folder called test_frags. Then I ran the script as:
    
    ./make_fragments.pl -rundir test_frags/ -verbose lig_0.fasta
    
    … and got this:
    
    FILENAME: lig_0.fasta
    
    Sequence: DDYLWGLEAGEGISDLFD
    
    Running sparks for phi, psi, and solvent accessibility predictions
    
    running psiblast for sequence: lig_0.fasta
    
    [blastpgp] WARNING: Unable to open nr.00.pin
    
    [blastpgp] WARNING: Unable to open nr.01.pin
    
    [blastpgp] WARNING: Unable to open nr.02.pin
    
    [blastpgp] WARNING: Unable to open nr.03.pin
    
    [blastpgp] WARNING: Unable to open nr.04.pin
    
    [blastpgp] WARNING: Unable to open nr.05.pin
    
    [blastpgp] WARNING: Unable to open nr.06.pin
    
    [blastpgp] WARNING: Unable to open nr.07.pin
    
    [blastpgp] WARNING: Unable to open nr.08.pin
    
    [blastpgp] WARNING: Unable to open nr.09.pin
    
    [blastpgp] WARNING: Unable to open nr.10.pin
    
    [blastpgp] WARNING: Unable to open nr.11.pin
    
    [blastpgp] WARNING: Unable to open nr.00.pin
    
    [blastpgp] WARNING: Unable to open nr.01.pin
    
    [blastpgp] WARNING: Unable to open nr.02.pin
    
    [blastpgp] WARNING: Unable to open nr.03.pin
    
    [blastpgp] WARNING: Unable to open nr.04.pin
    
    [blastpgp] WARNING: Unable to open nr.05.pin
    
    [blastpgp] WARNING: Unable to open nr.06.pin
    
    [blastpgp] WARNING: Unable to open nr.07.pin
    
    [blastpgp] WARNING: Unable to open nr.08.pin
    
    [blastpgp] WARNING: Unable to open nr.09.pin
    
    [blastpgp] WARNING: Unable to open nr.10.pin
    
    [blastpgp] WARNING: Unable to open nr.11.pin
    
    [blastpgp] WARNING: Unable to open nr.pin
    
    At line 180 of file phipsi_ss0.f
    
    Fortran runtime error: Bad real number in item 3 of list input
    
    Aborting: Can’t run first SS0 predictor
    
    Error in file: lig_0.fasta.phipsi
    
    Traceback (most recent call last):
    
    File “/mnt/data/yalmeida/Softwares/Rosetta/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 255, in run1
    
    buildinp(fphipsiss, fmat, finp)
    
    File “/mnt/data/yalmeida/Softwares/Rosetta/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 238, in buildinp
    
    seq1, ssec1, phipsi1, Fphipsi = rdphipsi(fphipsiss)
    
    File “/mnt/data/yalmeida/Softwares/Rosetta/tools/fragment_tools/sparks-x/bin/buildinp.py”, line 9, in rdphipsi
    
    for line in file(fn):
    
    IOError: [Errno 2] No such file or directory: ‘lig_0.fasta.phipsi’
    
    sparks failed!
    
    I have the nr files in the databases/ folder, obtained and processed after the uniref50 db.
    
    Regards
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