ERROR: Unused “free” argument specified: GDP.fa.tors

[Anonymous]

I have the following flags in my refinement flag file, I’m getting the error ERROR: Unused “free” argument specified: GDP.fa.tors, I’m not sure why! 

-extra_res_cen GTP.cen.params GDP.cen.params -extra_res_fa GTP.fa.params GDP.fa.params-extra_improper_file GTP.fa.tors GDP.fa.tors 

 

[Anonymous]

If that’s your actual command line, you’re missing a space between GDP.fa.params and -extra_improper_file.

[Anonymous]

 First off, you’re missing the space between the GDP.fa.params and the -extra_improper_file

Secondly, the different options in an options file need to be on different lines.  Because you’re starting a line with “GTP.fa.tors” it’s trying to recognize it as an option, rather than a parameter to the -extra_improper_file option. Your options file should look more like the following. (Including the line breaks)

 

-extra_res_cen GTP.cen.params GDP.cen.params

-extra_res_fa GTP.fa.params GDP.fa.params

-extra_improper_file GTP.fa.tors GDP.fa.tors

 

[Anonymous]

Ok, here’s my full script. It’s funny now I’m getting a different error below.

#!/bin/bash



$ROSETTA3/source/bin/rosetta_scripts.linuxgccrelease 

    -in::file: /home/labusr/Documents/starting_single_dimer.pdb 

    -parser::protocol /home/labusr/Documents/asymm_refine.xml 

    -parser::script_vars denswt=35 rms=1.5 reso=4.4 map=TetraAllPF_8nm_half1_b250_f4_4A_corr.mrc testmap=TetraAllPF_8nm_half2_b250_f4_4A_corr.mrc

    -ignore_unrecognized_res 

    -edensity::mapreso 4.4 

    -default_max_cycles 200 

    -edensity::cryoem_scatterers 

    -beta 

    -out::suffix _$1

    -crystal_refine

    -extra_res_cen GTP.cen.params GDP.cen.params 

    -extra_res_fa GTP.fa.params GDP.fa.params

    -extra_improper_file GTP.fa.tors GDP.fa.tors

 

 

core.init: Rosetta version rosetta.source.release-152:d6547f6858282e67c41356255dfdd63b0e7a75aa 2017-09-08 02:01:37.594540 from http://www.rosettacommons.org

core.init: command: /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease -in::file: /home/labusr/Documents/starting_single_dimer.pdb -parser::protocol /home/labusr/Documents/asymm_refine.xml -parser::script_vars denswt=35 rms=1.5 reso=4.4 map=TetraAllPF_8nm_half1_b250_f4_4A_corr.mrc testmap=TetraAllPF_8nm_half2_b250_f4_4A_corr.mrc -ignore_unrecognized_res -edensity::mapreso 4.4 -default_max_cycles 200 -edensity::cryoem_scatterers -beta -out::suffix _ -crystal_refine

core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1470792057 seed_offset=0 real_seed=1470792057

core.init.random: RandomGenerator:init: Normal mode, seed=1470792057 RG_type=mt19937

core.init: Resolved executable path: /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/rosetta_scripts.default.linuxgccrelease

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

protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter

protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs

protocols.jd2.PDBJobInputter: pushed /home/labusr/Documents/starting_single_dimer.pdb nstruct index 1

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from PDB /home/labusr/Documents/starting_single_dimer.pdb

core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 557 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 0.52 seconds.

core.import_pose.import_pose: [ ERROR ] File: /home/labusr/Documents/starting_single_dimer.pdb not found!



ERROR: Cannot open file "/home/labusr/Documents/starting_single_dimer.pdb"

ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 324

BACKTRACE:

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7f9a741e948f]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x389) [0x7f9a7868b1c9]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x50) [0x7f9a7868c330]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, bool, core::import_pose::FileType)+0x3b) [0x7f9a7868c51b]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0x3d5) [0x7f9a790cdd75]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x6aa) [0x7f9a790a805a]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x7f9a790a9f71]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x7f9a790816ba]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403408]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f9a721dec05]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403d4b]

Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'starting_single_dimer__0001'

Error: [ ERROR ]



[ ERROR ] EXCN_utility_exit has been thrown from: src/core/import_pose/import_pose.cc line: 324

ERROR: Cannot open file "/home/labusr/Documents/starting_single_dimer.pdb"





Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: starting_single_dimer__0001

protocols.jd2.JobDistributor: no more batches to process...

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds

Error: [ ERROR ] Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages

Error: [ ERROR ]

./A_asymm_refine.sh: line 14: -extra_res_cen: command not found

./A_asymm_refine.sh: line 15: -extra_res_fa: command not found

./A_asymm_refine.sh: line 16: -extra_improper_file: command not found

 

[Anonymous]

 

core.import_pose.import_pose: [ ERROR ] File: /home/labusr/Documents/starting_single_dimer.pdb not found!

 

Your argument to -s is wrong.  If the file exists it’s possible you don’t have permission to read it.

[Anonymous]

Thanks a lot it’s running now in a bash script, but I’m trying to call these commands using subprocess.call in Python. Here’s my Python script. I’m still getting unused free argument there:

 

    call(['/usr/local/rosettacommons/2017.08.59291/main/source/bin/rosetta_scripts.linuxgccrelease',

'-in::file:', structure,

'-parser::protocol', refinement_routine,

'-parser::script_vars', 'denswt=35', 'rms=1.5', 'reso=4.4',

'map=%s' %refinement_map,

'testmap=%s' %test_map,

'-in:ignore_unrecognized_res',

'-edensity::mapreso', '4.4',

'-default_max_cycles', '200',

'-edensity::cryoem_scatterers',

'-beta',

'-out::suffix', '_%s' %i,

'-crystal_refine',

'-extra_res_cen','GTP.cen.params', 'GDP.cen.params',

'-extra_res_fa','GTP.fa.params', 'GDP.fa.params',

'-extra_improper_file','GTP.fa.tors', 'GDP.fa.tors'])

 

 

Edit: never mind what I said above. It’s not working, this is what  Igot at the end of the log:

core.scoring.electron_density.ElectronDensity: Forcing apix to 1.375,1.375,1.375

protocols.electron_density.ReportFSC: FSC[mask=5.94209](10:4.4) = 0.098919 / 0.0967712

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: setting status to success

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================

protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================

protocols.jd2.JobDistributor: starting_single_dimer__0001 reported success in 4857 seconds

protocols.jd2.JobDistributor: no more batches to process...

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 4858 seconds

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

protocols::checkpoint: Deleting checkpoints of FastRelax

./A_asymm_refine.sh: line 14: -extra_res_cen: command not found

./A_asymm_refine.sh: line 15: -extra_res_fa: command not found

./A_asymm_refine.sh: line 16: -extra_improper_file: command not found

 

[Anonymous]

This is a python or other script error not a Rosetta error.

It’s not clear to me why `./A_asymm_refine.sh` is mentioned in the log file as it does not appear in the python snippet you have posted.  I assume you have a shell script calling a python script calling Rosetta and you have loose junk in the outermost shell script A_asymm_refine.  

If you are sure this is in python – I would preformat your argument to subprocess.call as one big string and print it, to ensure it comes out right and that you don’t have any loose endline characters in it from your variable substitutions.

[Anonymous]

First, I want to debug the bash script, becasuse it doesn’t seem to be working! It initially runs fine, then gives these errors ./”name of script”.sh: line 14: “flag”: command not found. I attached the script, it’s better to inspect it to verify the syntax is correct. Thanks a lot, I appreciate your help.

[Anonymous]

Bash needs all the arguments on one logical line.  Notice most of your arguments end in .  Those are escaping the newline character so that bash interprets it all as once logical line even though it prints on multiple lines.  Then notice some of the lines – the ones causing problems – are missing their trailing .  The last line should not have a as it is really the end of a line and thus should have an endline character.

[Anonymous]

Fantastic, now after fixing that stuff (sorry I’m familiar with python more than bash), I get the same error as in the python script (which makes more sense):

[labusr@luxor nucleotide_refienment]$ ./A_asymm_refine.sh

ERROR: ERROR: Unused "free" argument specified: GDP.fa.tors

Error: [ ERROR ] Exception caught by rosetta_scripts application:ERROR: ERROR: Unused "free" argument specified: GDP.fa.tors

Error: [ ERROR ]

[labusr@luxor nucleotide_refienment]$

 

Edit:

 

I contacted Frank, he told me to cat the two files. Thanks a lot for all of your help. 

[Anonymous]

I’ve never used -extra_improper_file.  If you look at the options documentation you will find https://www.rosettacommons.org/docs/latest/full-options-list that it takes a string, not a stringVector – in other words you are allowed only one file argument here, not arbitrarily many (like for extra_res_fa). 

If you need multiple of these files – you can probably concatenate them together.  You might need to delete the header in the second one to do that.  You might also need to manually resolve any duplicates.

-extra_improper_file <String>

Add extra parameters for improper torsions

[Author]

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