“sparks failed” error when running “make_fragments.pl”?

[Anonymous]

-Precision-7920-Tower:make_fragments.pl -verbose myfasta.fasta

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: /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!

Dear Friends, 

 

the above error comes when running “make_fragments.pl”. Can you please let me know how this can be solved? 

 

Thanks!

[Anonymous]

Hello,

as the error says:

sparks path length > 100 characters, which may cause internal errors. Try moving to a shorter path prefix.

sparks failed!

the poblem is that sparksX is hardcoded to look at only the first 100 or so characters of a file path.

/media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools/sparks-x/SPINE-X/weights/ss

so if you can, make a smylink to the tools folder much higher up in directory space.

ie something like:

ln -s /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/ /media/Deepak/rosetta_tools

or just move the tools folder ‘higher up’ and it will work.

 

make sure you run from /media/Deepka/rosetta_tools if you use that method though.it has to ‘think’ it’s a shorter path.

 

[Anonymous]

thanks! I did this:

 

ln -s /media/Deepak/NPRP10/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/ /media/Deepak/NPRP10/rosetta_tools

 

and then:

 

Precision-7920-Tower:/media/Deepak/NPRP10/rosetta_tools/tools/fragment_tools# perl make_fragments.pl -verbose myfasta.fasta

Use of uninitialized value $ENV{"FRAGMENT_PICKER_NUM_CPUS"} in int at make_fragments.pl line 35.

Use of uninitialized value $ENV{"BLAST_NUM_CPUS"} in int at make_fragments.pl line 41.

Use of uninitialized value $ENV{"PSIPRED_USE_weights_dat4"} in int at make_fragments.pl line 52.

Use of uninitialized value $ENV{"SLAVE_LAUNCHER_MAX_JOBS"} in int at make_fragments.pl line 71.

Use of uninitialized value $ENV{"SLAVE_MAX_WAIT"} in int at make_fragments.pl line 73.

Use of uninitialized value $ENV{"SLAVE_MAX_ATTEMPTS"} in int at make_fragments.pl line 74.

Use of uninitialized value $ENV{"PDB2VALL_IGNORE_ERRORS"} in int at 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/softwares/rosetta/rosetta_src_2019.31.60840_bundle/tools/fragment_tools

runid: t001_

sam: 0

samfile:

torsion_bin: 0

verbose: 1



FILENAME: t001_.fasta

Sequence: MAVGEIQISALPQAALPIDLSDIFHLKQGIEDKRCTLEQLLAPHSSLKNNPHGVTKTQIGLDNVINALQLVAANNLSDIVNVAEARANLQIMSSEEVNSLIQQHINDKSNPHNTTKAQVGLSNVQNWTTSNLYNEDADKYATARAVNNLYKAVQASYPVGTIHLSMNPANPSTYLICGGTWELVSKGRALVGYDSDSRPVGSTFGSQTTALTVNNIPAHTHSVYVTGGGHTHGATASISAFDYGTKGTTTFDYGTKTVSTYDYGNRTTSAAGLTQTTFINRGYADGGWRGLSVEGASYDPRATLTTANNHTHSVAIGAHNHTVGIGAHSHTVAIGSHNHSATVTVTGAGEHSHSGTTGPTGSGQAFSVEQPSFVLYVWQRTA

Running sparks for phi, psi, and solvent accessibility predictions

running psiblast for sequence: t001_.fasta

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!

 

It still takes the old path for some reason. Can you please let me know what am I doing wrong? thanks!

[Anonymous]

Hrm that’s odd… unfortunately it seems like you will have to remove the symlink and mv the folder there completely.  sorry : (

[Anonymous]

thanks! do I need to move only the “spaks-x” folder up the path or all folders; database (657 GB), psipred, csblast, blast. I mean all the folders generated by “install_dependencies.pl”? thanks for your suggestions!

[Anonymous]

Ok, it works now, I just played around with sym linking appropriate folders and finally it works. thanks!

[Anonymous]

Hello,

I am currently facing the exact problem you did. Would you be able to share exactly how you set up your symlinks? I tried the initial one suggested by danpf and it also failed for me as well. It would be extremley helpful and appreciated. Thanks!

[Author]

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