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Error when trying to thread target sequence over template pdbs, partial_thread.static.macosclangrelease not working properly

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Error when trying to thread target sequence over template pdbs, partial_thread.static.macosclangrelease not working properly
#1

*** note sure which category was appropriate for my question, chose Design but my Q pertains to threading for RosettaCM module***

Hello everyone,

 I am trying to perform the rosettaCM tutorial. As of now I am on part 2.B "Thread target sequence over three individual template sequences."

I am using version rosetta_bin_mac_2020.08.61146_bundle (3.12 release). I did not find the required file "~/rosetta_workshop/rosetta/main/source/bin/partial_thread.default.linuxgccrelease \" (I am assuming mine would be named .macosgccrelase or something along those lines)

closest thing I found with my realeas is a file called "partial_thread.static.macosclangrelease" and I initiated the threading process by running

$ ~/rosetta_bin_mac_2020.08.61146_bundle/main/source/bin/partial_thread.static.macosclangrelease \ -in:file:fasta 1u19.fasta -in:file:alignment 1u19_2rh1.grishin -in:file:template_pdb 2rh1.pdb

however I am getting the following error, with no .pdb.pdb output:

[ ERROR ]: Caught exception:

File: src/utility/options/OptionCollection.cc:315

ERROR: Unused "free" argument specified:  -in:file:fasta

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

 

The ROSETTA_CRASH.log itself has the following: 

 

##############################################################################################################

#

# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

#

 

[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2020.08+release.cb1cabafd74

[COMMIT_DATE]: 2020-02-22T06:57:31.821199

[APPLICATION]: UNKNOWN APPLICATION

[MODE]: Release

[EXTRAS]: default

[OS]: Apple Mac OS X

[COMPILER]: Clang version "9.0.0 (clang-900.0.39.2)"

[STDLIB]: libc++ version 4000

[START_OPTIONS]

NO OPTIONS SPECIFIED

[END_OPTIONS]

 

[START_BACKTRACE]: RAW_LIBC

0   partial_thread.static.macosclangrel 0x000000011170df4f backtrace_string(int) + 79

1   partial_thread.static.macosclangrel 0x000000011170de8c utility::excn::Exception::Exception(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) + 204

2   partial_thread.static.macosclangrel 0x00000001116cb536 utility::options::OptionCollection::load(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::list<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >&, bool) + 2422

3   partial_thread.static.macosclangrel 0x00000001116cbbda utility::options::OptionCollection::load(int, char* const*, bool) + 586

4   partial_thread.static.macosclangrel 0x000000010fd86352 core::init::init(int, char**) + 50

5   partial_thread.static.macosclangrel 0x000000010db72c67 main + 39

6   libdyld.dylib                       0x00007fff64db17fd start + 1

7   ???                                 0x0000000000000007 0x0 + 7

 

[END_BACKTRACE]

 

[FILE]: src/utility/options/OptionCollection.cc

[LINE]: 315

[START_MESSAGE]

ERROR: Unused "free" argument specified:  -in:file:fasta

 

[END_MESSAGE]

[END_CRASH_REPORT]

 

##############################################################################################################

#

# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

#

 

[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2020.08+release.cb1cabafd74

[COMMIT_DATE]: 2020-02-22T06:57:31.821199

[APPLICATION]: UNKNOWN APPLICATION

[MODE]: Release

[EXTRAS]: default

[OS]: Apple Mac OS X

[COMPILER]: Clang version "9.0.0 (clang-900.0.39.2)"

[STDLIB]: libc++ version 4000

[START_OPTIONS]

NO OPTIONS SPECIFIED

 

[END_OPTIONS]

 

[START_BACKTRACE]: RAW_LIBC

0   partial_thread.static.macosclangrel 0x000000010e8a0f4f backtrace_string(int) + 79

1   partial_thread.static.macosclangrel 0x000000010e8a0e8c utility::excn::Exception::Exception(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) + 204

2   partial_thread.static.macosclangrel 0x000000010e85e536 utility::options::OptionCollection::load(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::list<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >&, bool) + 2422

3   partial_thread.static.macosclangrel 0x000000010e85ebda utility::options::OptionCollection::load(int, char* const*, bool) + 586

4   partial_thread.static.macosclangrel 0x000000010cf19352 core::init::init(int, char**) + 50

5   partial_thread.static.macosclangrel 0x000000010ad05c67 main + 39

6   libdyld.dylib                       0x00007fff64db17fd start + 1

7   ???                                 0x0000000000000007 0x0 + 7

 

[END_BACKTRACE]

 

[FILE]: src/utility/options/OptionCollection.cc

[LINE]: 315

[START_MESSAGE]

ERROR: Unused "free" argument specified:  -in:file:fasta

 

[END_MESSAGE]

[END_CRASH_REPORT]

 

##############################################################################################################

#

# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

#

 

[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2020.08+release.cb1cabafd74

[COMMIT_DATE]: 2020-02-22T06:57:31.821199

[APPLICATION]: UNKNOWN APPLICATION

[MODE]: Release

[EXTRAS]: default

[OS]: Apple Mac OS X

[COMPILER]: Clang version "9.0.0 (clang-900.0.39.2)"

[STDLIB]: libc++ version 4000

[START_OPTIONS]

NO OPTIONS SPECIFIED

 

[END_OPTIONS]

 

[START_BACKTRACE]: RAW_LIBC

0   partial_thread.static.macosclangrel 0x000000010d610f4f backtrace_string(int) + 79

1   partial_thread.static.macosclangrel 0x000000010d610e8c utility::excn::Exception::Exception(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) + 204

2   partial_thread.static.macosclangrel 0x000000010d5ce536 utility::options::OptionCollection::load(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::list<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >&, bool) + 2422

3   partial_thread.static.macosclangrel 0x000000010d5cebda utility::options::OptionCollection::load(int, char* const*, bool) + 586

4   partial_thread.static.macosclangrel 0x000000010bc89352 core::init::init(int, char**) + 50

5   partial_thread.static.macosclangrel 0x0000000109a75c67 main + 39

6   libdyld.dylib                       0x00007fff64db17fd start + 1

 

[END_BACKTRACE]

 

[FILE]: src/utility/options/OptionCollection.cc

[LINE]: 315

[START_MESSAGE]

ERROR: Unused "free" argument specified:  -in:file:fasta

 

[END_MESSAGE]

[END_CRASH_REPORT]

 

##############################################################################################################

#

# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

#

 

[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2020.08+release.cb1cabafd74

[COMMIT_DATE]: 2020-02-22T06:57:31.821199

[APPLICATION]: UNKNOWN APPLICATION

[MODE]: Release

[EXTRAS]: default

[OS]: Apple Mac OS X

[COMPILER]: Clang version "9.0.0 (clang-900.0.39.2)"

[STDLIB]: libc++ version 4000

[START_OPTIONS]

NO OPTIONS SPECIFIED

 

[END_OPTIONS]

 

[START_BACKTRACE]: RAW_LIBC

0   partial_thread.static.macosclangrel 0x000000010d86af4f backtrace_string(int) + 79

1   partial_thread.static.macosclangrel 0x000000010d86ae8c utility::excn::Exception::Exception(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) + 204

2   partial_thread.static.macosclangrel 0x000000010d828536 utility::options::OptionCollection::load(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::list<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >&, bool) + 2422

3   partial_thread.static.macosclangrel 0x000000010d828bda utility::options::OptionCollection::load(int, char* const*, bool) + 586

4   partial_thread.static.macosclangrel 0x000000010bee3352 core::init::init(int, char**) + 50

5   partial_thread.static.macosclangrel 0x0000000109ccfc67 main + 39

6   libdyld.dylib                       0x00007fff64db17fd start + 1

7   ???                                 0x0000000000000007 0x0 + 7

 

[END_BACKTRACE]

 

[FILE]: src/utility/options/OptionCollection.cc

[LINE]: 315

[START_MESSAGE]

ERROR: Unused "free" argument specified:  -in:file:fasta

 

[END_MESSAGE]

[END_CRASH_REPORT]

Anyhelp would be greatly appreciated!

-DGR95

PS. I have had similar issues with the other provided scripts (ex. clean_pdb.py, and scons.py) but found working duplicate code in other directories than the ones listed in the tutorial (except for scons.py, i decided to spare me the headache and instead downloaded the  rosetta3 + macos binaries release) . Not sure if this is my issue but I dont think so. I have been checking my output/results after each step with the provded files in  /rosetta_bin_mac_2020.08.61146_bundle/demos/tutorials/rosetta_cm/1_setup and they are identical to the tutorial set. 

UPDATE:I figured it out, error was caused by a space after the backward slash "\". Formatting in pdf split the code in half. Correct code should be 

$ ~/rosetta_bin_mac_2020.08.61146_bundle/main/source/bin/partial_thread.static.macosclangrelease \-in:file:fasta 1u19.fasta -in:file:alignment 1u19_2rh1.grishin -in:file:template_pdb 2rh1.pdb

Category: 
Post Situation: 
Wed, 2020-04-15 14:42
DGR95