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

[Anonymous]

I hope this isn’t a repost but I couldn’t find anything here, I found a similar post on minirosetta but it wasn’t solved. I built Rosetta and tried to run abinitio in the rosetta_demos using this command /rosetta3.4/rosetta_demos/abinitio$ ../../rosetta_source/bin/AbinitioRelax.linuxgccrelease -in::file::fasta ./input_files/1elwA.fasta

this is my script:
core.init: Mini-Rosetta version unknown from unknown
core.init: command: ../../rosetta_source/bin/AbinitioRelax.linuxgccrelease -in::file::fasta input_files/1elwA.fasta
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=390087245 seed_offset=0 real_seed=390087245
core.init.random: RandomGenerator:init: Normal mode, seed=390087245 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /home/yamoahlab/Documents/ryan protein modeling/rosetta3.4/rosetta_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 1980 residue types
ERROR: Value of inactive option accessed: -in:file:frag9

os ubuntu 12.04 LTS
rosetta 3.4 downloaded from bundle academic_user

not sure if this is important but I just fixed this problem of ROSETTA3_DB not defined by entering this code:
export ROSETTA3_DB=/home/yamoahlab/Documents/ryan protein modeling/rosetta3.4/rosetta_database/

sorry if this is beginner stuff I’m only taken a couple beginner classes and I’m trying to teach myself programming so details would be nice.

Thanks for your help in advance

[Anonymous]

You haven’t passed Rosetta any fragment files. Rosetta is trying to read your fragment files from the command line option frag9, but you didn’t pass frag9, so it gives up and quits. Rosetta requires fragment files to have secondary structure samples with which to build proteins (try reading the Rohl review in Methods in Enzymology (2003 or 2004), or its references, to learn about fragments and the ab initio algorithm).

The simplest way to generate fragment files is to use the Robetta webserver: http://robetta.bakerlab.org/

[Anonymous]

thanks I got the sample to work now, however I do have a question about the robetta server. When I submitted a sequence and I am getting an ETC of 723 days, which is too long to wait. I have generated a fragment file from PHYRE2 but most of the protein is 60% in disorder. Do you know how to either cut down the ETC time and how their priority system works.I have been doing protein ligand binding using DOCK6.4 but now I’m trying to so a protein-protein problem for a paper that is being submitted soon and there is no crystal structure for my second protein, any other suggestions for generating frag files as well?

[Anonymous]

Thanks for the clarification, I do have one last question (hopefully). After I fixed this problem I ran into a header problem. When I try the tutorial for abinitio and type in the correct code it runs for a couple seconds and finally throws a HEADER error and exits at line 375 for SS_Killhairpins_info.cc. I tried compiling this program but when I did it said the header could not be found becaue the path was core/scoring/SS_Killhairpins.hh was incomplete. I’ve been editing the files one by one to complete the pathway so it looks like this /home/…/core/source/SS_Killhairpins.hh. I know this is a terrible idea because I will never be able to move anything but it was the only one I had. I would then compile to find the next incomplete pathway, this still is not done and has already taken me several hours. is there an easier way to fix this problem? I want to set up rosetta on another computer as well that is initialized in a similar way but I am very hesitant to even think about doing this again. especially because I want to adjust the source code and probably make several versions and once I do I would have to change everything again.

[Anonymous]

So I did that all last night, unpacked another copy of rosetta and I also did this on another computer that is running the same operating system. both are having the same problem. I did find a way to compile with g++ -I to give it the pathway to see where it really was failing and it seems to inport all the headers fine and throws an error of ld exit 1 status which according to other forums means no input files and this is expected, but the header files were imported. I made a script_demo that I run from my abinitio file which i have copied from rosetta_demos to rosetta_source for ease and it looks like this:
../bin/AbinitioRelax.linuxgccrelease -database ../rosetta_database -in:file:fasta input_files/1elwA.fasta -in:file:frag3 input_files/aa1elwA03_05.200_v1_3 -in:file:frag9 input_files/aa1elwA09_05.200_v1_3 -abinitio:relax -relax:fast -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -use_filters true -psipred_ss2 input_files/1elwA.psipred_ss2 -kill_hairpins input_files/1elwA.psipred_ss2 -out:file:silent 1elwA_silent.out -nstruct 10

http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d0/dd9/abinitio.html
(this is code from the abinitio manual found above)

I have tried this from the original location as well rosetta_demos/abinitio and just changed the file paths, every time i’m getting the same error. I’ll post all of my code here

core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1514320327 seed_offset=0 real_seed=1514320327
core.init.random: RandomGenerator:init: Normal mode, seed=1514320327 RG_type=mt19937
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 1980 residue types
core.io.fragments: reading fragments from file: abinitio/input_files/aa1elwA09_05.200_v1_3 …
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file abinitio/input_files/aa1elwA09_05.200_v1_3
core.io.fragments: reading fragments from file: abinitio/input_files/aa1elwA03_05.200_v1_3 …
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file abinitio/input_files/aa1elwA03_05.200_v1_3
core.fragment: compute strand/loop fractions for 117 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.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
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.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
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/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/MembranePotential/CEN6_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.txt
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
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1

ERROR: [ERROR] invalid header input for kill_hairpins file.
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 375

I also tested one last thing even though I know it was also a bad idea but I was interested. I copied all my files that include the headers to /usr/include (where g++/gcc looks for headers) and ran the programs under root, it compiled with the command g++ SS_Kilhairpins_Info.cc so I know it found the files without the path addition of -I but when I ran the code again I still get the same error.

Sorry if this is beginner stuff but I’ve been working on trying to get this program running for over 2 weeks now by searching and googling errors, finally I broke down and asked here to see if you can guys can help me.
I built from rosetta_source using this line:
scons bin mode=release

it completed building the targes and the only error I saw was for git, but as I understand that repository system is only for versioning and That isn’t important to me right now and shouldn’t affect the ability or rosetta operating. Again this is happening on two computers with ubuntu 12.04 LTS, any ideas on how to fix the runtime error?

[Anonymous]

Thank you very much, I thought it was a good idea to try to compile just to see what was going on in the code, i knew it wouldn’t necessarily fix the problem. I’m trying to teach myself how to use these predicting and modeling programs as well as identify programming error sources so thank you again for you help.

Ryan

[Anonymous]

I have utilized the robetta server to get my protein model, after a month of submission i have got an ETC status error. I have waited for a month to get results unfortunately it showing error. Please help me out to retrieve my protein model. And my user id 49163

[Anonymous]

The fragment server has no wait queue: http://robetta.bakerlab.org/fragmentqueue.jsp?p=1&rpp=15&Notes=&Email=&Host=&UserName=

I suspect you have submitted to the modeling queue instead (http://robetta.bakerlab.org/queue.jsp?p=1&). The wait time here is generally ridiculous because it is offered for free but expensive to provide and thus falls to the tragedy of the commons. The way to jump the queue is to have your own supercomputer and run it yourself, which is exactly what you are trying to do!

[Anonymous]

The _runtime_ problem you observed with the first few lines of your kill_hairpins data file has no bearing whatsoever on the _compilation_ of the code that interprets the file (SS_Killhairpins_Info.cc/hh). You should revert the changes you made to the code itself in re-pathing SS_Killhairpins_Info.hh. Changing the paths for SS_Killhairpins_Info.hh will not have any affect on the error “ERROR: [ERROR] invalid header input for kill_hairpins file.” that you were seeing, because that is a runtime error, and you are attempting to repair a compile-time error that didn’t occur. (Changing the logic of how SS_Killhairpins_Info.cc actually reads the supplied killhairpins file could prevent/alter this error.)

If you’ve made too many changes to track, just blow the whole copy of Rosetta away and un-tar from your download again. Actually, if you just un-tar into the directory it’s already in, it should just overwrite the repathed files and when you recompile it should compile correctly.

[Anonymous]

Let me reiterate: this is not a compilation error, it’s a runtime error.

I don’t do ab initio and have never used the code in question, but Rocco’s post on fixing the problem with kill_hairpins files has worked for many other users: http://www.rosettacommons.org/content/killhairpin-error#comment-4672

Are you actually intending to use a kill_hairpins file? The demo works for me, but doesn’t actually use that flag.

[Anonymous]

I’m happy to help – I was just frustrated to see a user put so much effort into something I knew wouldn’t work. I don’t want you wasting your time…

[Anonymous]

I have utilized the robetta server to get my protein model, after a month of submission i have got an ETC status error. I have waited for a month to get results unfortunately it showing error. Please help me out to retrieve my protein model. And my user id 49163

[Author]

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