Error running Abinitio relax with @flags

[Anonymous]

Dear Rosetta user’s,

I’d tried to run an abinitio fast relax employing the option @data with my system as it was pointed by documentation (https://www.rosettacommons.org/docs/latest/rosetta_basics/running-rosetta-with-options#running-rosetta-via-mpi) and the program gave me this error message [1]. Afterwards, I tried to run again (explicitly defining at the command line the same options that I’d included at my data file) and Rosetta run fine [2]. Until now I’m wondering what wrong I’d made with my data file that I couldn’t to run abinitio fast relax through @data option. Anyone could help me with this error?

Regards.

[1] samuel@jaguatirica:~/Lais/n$ AbinitioRelax.linuxgccrelease @data

core.init: Rosetta version exported  from http://www.rosettacommons.org

core.init: command: AbinitioRelax.linuxgccrelease @data

core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1118337764 seed_offset=0 real_seed=1118337764

core.init.random: RandomGenerator:init: Normal mode, seed=1118337764 RG_type=mt19937

core.init: found database environment variable ROSETTA3_DB: /home/tacio/Install/rosetta_src_2015.05.57576_bundle/main/database

ERROR: Error: can’t read sequence! Use -in::file::fasta sequence.fasta or -in::file::native native.pdb!

ERROR:: Exit from: src/protocols/abinitio/AbrelaxApplication.cc line: 490

/home/tacio/Install/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.2/64/x86/gcc/4.6/default/libutility.so(print_backtrace()+0x1e) [0x2ba754f5bd1e]

/home/tacio/Install/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.2/64/x86/gcc/4.6/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0xb9) [0x2ba754f5ba99]

/home/tacio/Install/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.2/64/x86/gcc/4.6/default/libprotocols_b.5.so(protocols::abinitio::AbrelaxApplication::setup()+0x163f) [0x2ba75367c8bf]

/home/tacio/Install/rosetta_src_2015.05.57576_bundle/main/source/build/src/release/linux/3.2/64/x86/gcc/4.6/default/libprotocols_b.5.so(protocols::abinitio::AbrelaxApplication::run()+0x199) [0x2ba7536966f9]

AbinitioRelax.linuxgccrelease() [0x401f0a]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x2ba75573476d]

AbinitioRelax.linuxgccrelease() [0x402175]

Exception :

[ERROR] EXCN_utility_exit has been thrown from: src/protocols/abinitio/AbrelaxApplication.cc line: 490

ERROR: Error: can’t read sequence! Use -in::file::fasta sequence.fasta or -in::file::native native.pdb!

protocols::checkpoint: Deleting checkpoints of Abrelax

[2] samuel@jaguatirica:~/Lais/n$ AbinitioRelax.linuxgccrelease -database /home/tacio/Install/rosetta_src_2015.05.57576_bundle/main/database -in::file::fasta /home/samuel/Lais/n/t000_.fasta -in::file::frag3 /home/samuel/Lais/n/aat000_03_05.200_v1_3 -in::file::frag9 /home/samuel/Lais/n/aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -use_filters true -out:file:silent bamil13_10.out -nstruct 10 -constant_seed -jran 1234567 -psipred_ss2 /home/samuel/Lais/n/t000_.psipred -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.7 -abinitio::rg_reweight 0.5 -seed_offset 10

core.init: Rosetta version exported  from http://www.rosettacommons.org

core.init: command: AbinitioRelax.linuxgccrelease -database /home/tacio/Install/rosetta_src_2015.05.57576_bundle/main/database -in::file::fasta /home/samuel/Lais/n/t000_.fasta -in::file::frag3 /home/samuel/Lais/n/aat000_03_05.200_v1_3 -in::file::frag9 /home/samuel/Lais/n/aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -use_filters true -out:file:silent bamil13_10.out -nstruct 10 -constant_seed -jran 1234567 -psipred_ss2 /home/samuel/Lais/n/t000_.psipred -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.7 -abinitio::rg_reweight 0.5 -seed_offset 10

core.init: Constant seed mode, seed=1234567 seed_offset=10 real_seed=1234577

core.init.random: RandomGenerator:init: Normal mode, seed=1234577 RG_type=mt19937

protocols.abinitio.AbrelaxApplication: read fasta sequence: 42 residues

DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIT

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …

core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.  Created 1042 residue types

core.io.fragments: reading fragments from file: /home/samuel/Lais/n/aat000_09_05.200_v1_3 …

core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…

core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file /home/samuel/Lais/n/aat000_09_05.200_v1_3

core.io.fragments: reading fragments from file: /home/samuel/Lais/n/aat000_03_05.200_v1_3 …

core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…

core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /home/samuel/Lais/n/aat000_03_05.200_v1_3

core.fragment: compute strand/loop fractions for 42 residues…

protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..

basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt

basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt

basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt

basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt

basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth

basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth

core.scoring: ATOM_VDW set to CENTROID_ROT

basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp

basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4

basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt

basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt

basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt

basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt

core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40

basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt

core.scoring.CartesianBondedEnergy: Read 770 bb-independent lengths.

basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt

core.scoring.CartesianBondedEnergy: Read 1464 bb-independent angles.

basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt

core.scoring.CartesianBondedEnergy: Read 2127 bb-independent torsions.

core.scoring: ATOM_VDW set to CENTROID_ROT

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013

core.scoring.etable: Starting energy table calculation

core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well

core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)

core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)

core.scoring.etable: Finished calculating energy tables.

protocols.jobdist.JobDistributors: Looking for an available job: 1 1  1

protocols.relax.ClassicRelax: Setting up default relax setting

protocols::checkpoint: Deleting checkpoints of ClassicRelax

protocols.abinitio:

===================================================================

   Stage 1                                                         

   Folding with score0 for max of 20000

protocols.abinitio: Replaced extended chain after 20 cycles.

protocols.moves.TrialCounter: ClassicFragmentM trials=     20;  accepts= 0.9000;  energy_drop/trial=   0.00413

protocols.abinitio:

---

 Scores                       Weight   Raw Score Wghtd.Score

---

 vdw                          0.100       0.826       0.083

---

 Total weighted score:                        0.083

[Anonymous]

What was the format of the file you were passing as the “@” file?

It’s not really “@data” but rather “@options“, where the file specified after the @ symbol contains the same contents as the commandline options. It can be a little finiky, though. There’s a nested format, but you have to be careful about indentation levels and not mixing tabs and spaces. Also, stray non-printing characters (e.g. Windows-style line endings) can also cause trouble.

[Anonymous]

I am getting error while runnig this command : Rosetta/main/source/bin/AbinitioRelax.linuxgccrelease @flags

Flag :    -in:file:fasta ./input_files/1elwA.fasta

core.init: Rosetta version exported  from http://www.rosettacommons.org

core.init: command: rosetta/main/source/bin/AbinitioRelax.linuxgccrelease -in:file:fasta ./rosetta/demos/public/abinitio/input/1elwA.fasta

core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=620059290 seed_offset=0 real_seed=620059290

core.init.random: RandomGenerator:init: Normal mode, seed=620059290 RG_type=mt19937

core.init: Resolved executable path: /home/george/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/AbinitioRelax.static.linuxgccrelease

core.init: Looking for database based on location of executable: /home/george/rosetta/main/database/

protocols.abinitio.AbrelaxApplication: read fasta sequence: 117 residues

EQVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEAR

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …

core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.  Created 1042 residue types

core.chemical.ResidueTypeSet: Total time to initialize 0.03 seconds.

ERROR: Value of inactive option accessed: -in:file:frag9

 

[Anonymous]

Dear Rocco,

I’m used to work in Linux native machines (Ubuntu 14.0 LTS) and I’m using the vim editor to build all my files, including data. I guess the vim files was ASCII files. I’ll check my data file to search about non-printing characters also.

Regards.

[Anonymous]

Dear Rocco,

I’d checked my data file and the white spaces gave me the previous error message when I run Rosetta abinitio relax.

Thanks a lot!

[Anonymous]

“Value of inactive option accessed” means that Rosetta tried to get (access) the value of an option, but it wasn’t given on the commandline or the flags file (it’s “inactive”). You would need to give an appropriate setting for the listed option (in this case, give the filename of an appropriate fragment file to -in:file:frag9).

[Anonymous]

Thank you for your reply, as you said in this case, I have to give the filename of an appropriate fragment file to -in:file:frag9. However i didn’t  get which filename you are asking for and how to do that. if you will elaborate then it will be extremely helpfull for me.

below I am mentioning what exactaly I am doing :

I have created one directory of name test in desktop in that one more directory input_files where i have kept all input files that is given in demo input_files of rosetta, to run these  i am  using this command : “rosetta/main/source/bin/AbinitioRelax.linuxgccrelease -in:file:fasta ./Desktop/test/input_files/1elwA.fasta” as given instructions in read me file .

please let me know if I am doing anything wrong.

Thanking you.

 

[Anonymous]

Rosetta ab inito uses a “fragment insertion” based approach to build the structure of the protein. (If you haven’t already, I strongly encourage you to read up on some of the published papers about it.) That is, using the sequence and predicted secondary structure of the protein you wish to model, you look through the PDB to find already existing proteins which are similar, at least over small regions. This is normally done for a number of different sized regions – typically 3 amino acid and 9 amino acid sized fragments. You then “borrow” the backbone conformations of those small existing protein regions, and assemble them to get a possible structure of your protein of interest. But you don’t have just a single possibility for any small segment, instead you have a number of possibilities, and Rosetta tries multiple different combinations of them, guided by an scoring function to pick out the best one.

A key point from your perspective is that the search for existing protien fragments and the assembly into a single protein are split into separate phases. The AbinitioRelax.linuxgccrelease program handles the assembly and scoring phase. But to do this, it needs to have information about the fragments which match your sequence – that is, what parts of the existing PDBs should it combine together? It gets this information from fragment files.

The recommended way of obtaining fragment files (at least for academic users) is with the Robetta server (http://robetta.bakerlab.org/). Given a sequence, it will generate 3-mer and 9-mer fragment files. These generated files can them be passed to the AbinitioRelax.linuxgccrelease program using the approriate options, in addtion to the options which specify the fasta sequence you wish to model. 

These options can either be specified directly on the commandline, or Rosetta also has the ability to load the options from a text file, with the Rosetta-specific “@options_filename” syntax.

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