Rosetta make_fragments.pl error?

[Anonymous]

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.

 

 

[Anonymous]

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!

[Anonymous]

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!

 

[Anonymous]

I figured out the answer. thanks!

[Author]

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