Rosetta fragment tools installation error

[Anonymous]

Dear Friends,

 

I am trying to install rosetta on my local system, but facing issues because of CSBLAST. The latest rosetta bunble I downloaded from rosetta website is : rosetta_src_2019.31.60840_bundle.

After that, since I want to perform “ab initio structure prediction”, I am following this tutorial:

https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction

In this tutorial, there is a “fragment picking” tutorial:: https://www.rosettacommons.org/demos/latest/public/fragment_picking/README

I am following this tutorila to make fragments for de novo structure prediction; however, I am stuck at this step:

 

• Put this vall in the flags:

  $ <path-to-Rosetta>/main/database/sampling/filtered.vall.dat.2006-05-05.gz

  Update the flags with your correct database location

• Run the picker like this:

To accomplish this step, I went to  “tools/fragment_tools/” folder of the bundle and ran “install-dependencies.pl”, but it gave me error for CSBLAST package saying:

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/application.o application.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/aa.o aa.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/dna.o dna.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/log.o log.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/getopt_pp.o getopt_pp.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/blosum_matrix.o blosum_matrix.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/assert_helpers.o assert_helpers.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/utils.o utils.cc

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS=””-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64″” -fno-strict-aliasing -DVERSION=””2.2.3″” -DBUILD_HOST=””`hostname`”” -DBUILD_TIME=””`date`”” -DCOMPILER_VERSION=””`/usr/bin/g++ -v 2>&1 | tail -1`”” -I$HOME/include -c -o ../build/csblast_app.o csblast_app.cc

In file included from csblast_app.cc:21:0:

alignment-inl.h: In function ‘Vector<double> cs::PositionSpecificWeightsAndDiversity(const cs::Alignment<Abc>&, Matrix<double>&)’:

alignment-inl.h:842:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]

             if (ncoli < kMinCols)  // number of columns in subalignment insufficient?

                ^

In file included from pseudocounts-inl.h:22:0,

                 from context_library.h:26,

                 from csblast_app.cc:25:

pseudocounts.h: At global scope:

pseudocounts.h:172:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kNormalize’ of non-integral type [-fpermissive]

     static const double kNormalize           = 1e-5; // Normalization threshold.

                         ^~~~~~~~~~

pseudocounts.h:173:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffParamMin’ of non-integral type [-fpermissive]

     static const double kTargetNeffParamMin  = 0.0;  // Minimal paramater value for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~~~~~~

pseudocounts.h:174:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffParamMax’ of non-integral type [-fpermissive]

     static const double kTargetNeffParamMax  = 1.0;  // Maximal parameter value for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~~~~~~

pseudocounts.h:175:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffParamInit’ of non-integral type [-fpermissive]

     static const double kTargetNeffParamInit = 0.5;  // Initial parameter value for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~~~~~~~

pseudocounts.h:176:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffEps’ of non-integral type [-fpermissive]

     static const double kTargetNeffEps       = 0.01; // Convergence threshold for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~

pseudocounts.h: In instantiation of ‘class cs::Pseudocounts<cs::AA>’:

csblast_app.cc:327:38:   required from here

pseudocounts.h:172:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kNormalize’ of non-integral type [-fpermissive]

     static const double kNormalize           = 1e-5; // Normalization threshold.

                         ^~~~~~~~~~

pseudocounts.h:173:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffParamMin’ of non-integral type [-fpermissive]

     static const double kTargetNeffParamMin  = 0.0;  // Minimal paramater value for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~~~~~~

pseudocounts.h:174:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffParamMax’ of non-integral type [-fpermissive]

     static const double kTargetNeffParamMax  = 1.0;  // Maximal parameter value for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~~~~~~

pseudocounts.h:175:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffParamInit’ of non-integral type [-fpermissive]

     static const double kTargetNeffParamInit = 0.5;  // Initial parameter value for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~~~~~~~

pseudocounts.h:176:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffEps’ of non-integral type [-fpermissive]

     static const double kTargetNeffEps       = 0.01; // Convergence threshold for adjusting to the target Neff.

                         ^~~~~~~~~~~~~~

Makefile:129: recipe for target ‘../build/csblast_app.o’ failed

make: *** [../build/csblast_app.o] Error 1

 

Hence, “install_dependencies.pl” did not work, so I cannot run “make_fragments.pl”, and thus, no vall files. could you please let me know how can I resolve this issue? I need to perform ab initio structure prediction for a 382 residue long phage tail protein. Your suggestions are very welcome.

 

Regards

 

[Anonymous]

Hello,

I believe your gcc/g++ version is too new, I don’t see the error with gcc5.4/g++5.4

 

as an alternative you could have the robetta server build your fragments for you here:

http://robetta.bakerlab.org/fragmentsubmit.jsp

[Anonymous]

Yes that was the reason. I degraded gcc to version 5.5 and it worked. 

[Author]

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