make_fragments.pl error

[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.

 

[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!

 

[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

[Author]

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