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

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ERROR: Unused "free" argument specified: GDP.fa.tors
#1

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 

 

Post Situation: 
Fri, 2018-06-15 11:27
ahmadkhalifa

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

Fri, 2018-06-15 11:35
smlewis

 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

 

Fri, 2018-06-15 11:36
rmoretti

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::s /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::s /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

 

Mon, 2018-06-18 06:55
ahmadkhalifa

 

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.

Mon, 2018-06-18 08:03
smlewis

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::s', 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

 

Mon, 2018-06-18 12:32
ahmadkhalifa

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.

Mon, 2018-06-18 13:12
smlewis

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.

File attachments: 
Mon, 2018-06-18 14:07
ahmadkhalifa

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.

Mon, 2018-06-18 14:58
smlewis

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. 

Tue, 2018-06-19 09:58
ahmadkhalifa

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
Tue, 2018-06-19 09:28
smlewis