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Rosetta make_fragments.pl error?

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Rosetta make_fragments.pl error?
#1
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Dear Friends,

 

I am trying to perform ab initio structure prediction by following the tutorial:

https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction

In this tutorial, there is a "fragment picking" tutorial:: https://www.rosettacommons.org/demos/latest/public/fragment_picking/README

I am following this tutorila to make fragments for de novo structure prediction:

 

  • Put this vall in the flags:

    $ <path-to-Rosetta>/main/database/sampling/filtered.vall.dat.2006-05-05.gz

    Update the flags with your correct database location

  • Run the picker like this:

 

I installed all dependencies using "install_dependencies.pl", and now trying to make fragmensts using "make_fragments.pl". when running the script it gives me this error: 

softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl -verbose c600m2-tail-fiber-sequence.fasta
Use of uninitialized value $ENV{"FRAGMENT_PICKER_NUM_CPUS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 35.
Use of uninitialized value $ENV{"BLAST_NUM_CPUS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 41.
Use of uninitialized value $ENV{"PSIPRED_USE_weights_dat4"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 52.
Use of uninitialized value $ENV{"SLAVE_LAUNCHER_MAX_JOBS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 71.
Use of uninitialized value $ENV{"SLAVE_MAX_WAIT"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 73.
Use of uninitialized value $ENV{"SLAVE_MAX_ATTEMPTS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 74.
Use of uninitialized value $ENV{"PDB2VALL_IGNORE_ERRORS"} in int at softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 80.
Only alphanumeric characters, . and _ are allowed in the filename.

 

Can ypou please let me know what could be the issue here? and how this can be solved? thanks.

 

 

Category: 
Structure prediction
Post Situation: 
Unsolved
Mon, 2019-09-02 07:51
Danielsebas
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This is just some old weird code...

change the name of your fasta file to something stupid and simple

like:

myfasta.fasta

 

and you shouldn't see this error!

Mon, 2019-09-02 10:06
danpf
(Reply to #3)
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Thanks it worked and the program ran, but then I face this issue of "sparks failed": Can you please let me know how this can be solved? thanks!

  

Precision-7920-Tower:/media/Deepak/NPRP10/nprp10-data/lamb-data/c600m2-tail-fiber-model/rosetta/rosetta-abintio-prediction# /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl -verbose myfasta.fasta 
Use of uninitialized value $ENV{"FRAGMENT_PICKER_NUM_CPUS"} in int at /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 35.
Use of uninitialized value $ENV{"BLAST_NUM_CPUS"} in int at /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 41.
Use of uninitialized value $ENV{"PSIPRED_USE_weights_dat4"} in int at /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 52.
Use of uninitialized value $ENV{"SLAVE_LAUNCHER_MAX_JOBS"} in int at /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 71.
Use of uninitialized value $ENV{"SLAVE_MAX_WAIT"} in int at /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 73.
Use of uninitialized value $ENV{"SLAVE_MAX_ATTEMPTS"} in int at /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 74.
Use of uninitialized value $ENV{"PDB2VALL_IGNORE_ERRORS"} in int at /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/make_fragments.pl line 80.
no id specified. parsing filename instead.
cannot parse id from filename so using 't001_'
ID: t001 CHAIN: _
File for psipred not found! Generating from scratch instead.
picking fragments with options:
                       DEBUG: 1
            add_pdbs_to_vall: 
                       chain: _
                     cleanup: 1
             csbuild_profile: 0
exclude_homologs_by_pdb_date: 0
                           f: myfasta.fasta
                   fastafile: t001_.fasta
                       frags: 1
                        homs: 1
                          id: t001
                n_candidates: 1000
                     n_frags: 200
             old_name_format: 0
                      porter: 0
                  porterfile: 
                     psipred: 1
                 psipredfile: 
                      rundir: /media/Deepak/NPRP10/nprp10-data/lamb-data/c600m2-tail-fiber-model/rosetta/rosetta-abintio-prediction
                       runid: t001_
                         sam: 0
                     samfile: 
                 torsion_bin: 0
                     verbose: 1
--------------------------------------------------------------------------------

FILENAME: t001_.fasta
Sequence: MAVGEIQISALPQAALPIDLSDIFHLKQGIEDKRCTLEQLLAPHSSLKNNPHGVTKTQIGLDNVINALQLVAANNLSDIVNVAEARANLQIMSSEEVNSLIQQHINDKSNPHNTTKAQVGLSNVQNWTTSNLYNEDADKYATARAVNNLYKAVQASYPVGTIHLSMNPANPSTYLICGGTWELVSKGRALVGYDSDSRPVGSTFGSQTTALTVNNIPAHTHSVYVTGGGHTHGATASISAFDYGTKGTTTFDYGTKTVSTYDYGNRTTSAAGLTQTTFINRGYADGGWRGLSVEGASYDPRATLTTANNHTHSVAIGAHNHTVGIGAHSHTVAIGSHNHSATVTVTGAGEHSHSGTTGPTGSGQAFSVEQPSFVLYVWQRTA
Running sparks for phi, psi, and solvent accessibility predictions
t001_.fasta.pssm exists
At line 239 of file phipsi_ss0.f (unit = 77, file = '/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/SPINE-X/weights/ss')
Fortran runtime error: End of file
Aborting: Can't run first SS0 predictor
Error in file: t001_.fasta.phipsi
Traceback (most recent call last):
  File "/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py", line 255, in run1
    buildinp(fphipsiss, fmat, finp)
  File "/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/bin/buildinp.py", line 238, in buildinp
    seq1, ssec1, phipsi1, Fphipsi = rdphipsi(fphipsiss)
  File "/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_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: 't001_.fasta.phipsi'
sparks path length > 100 characters, which may cause internal errors. Try moving to a shorter path prefix.
sparks failed!

 

Tue, 2019-09-03 03:47
Danielsebas
(Reply to #4)
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I figured out the answer. thanks!

Thu, 2019-09-05 03:35
Danielsebas