error when using script best_ifaceE.py

[Anonymous]

Hi I have output my ligand-docked pdbs in silent out as both pdbs and in binary but regardless when I run the script to identify the top 10 percent based on IF delta score I get the following error.

 

FILE]: src/protocols/jd2/AtomTreeDiffJobInputter.cc

[LINE]: 132

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: No valid input structures found for AtomTreeDiff file.

 

 

 

[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.cb1caba

[COMMIT_DATE]: 2020-02-22T18:49:33.865989

[APPLICATION]: /share/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/bin/extract_atomtree_diffs.mpi.linuxgccrelease

[MODE]: Release

[EXTRAS]: mpi (OpenMPI 3.1.3) 

[OS]: GNU/Linux

[COMPILER]: GCC version “4.8.5 20150623 (Red Hat 4.8.5-39)”

[STDLIB]: libstdc++ version 20150623

[START_OPTIONS]

 -in:path:database=/share/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/database/ -in:file:s=silent.out -in:file:extra_res_fa=VK5.params

 

[END_OPTIONS]

 

[START_BACKTRACE]: RAW_LIBC

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libcore.6.so(backtrace_string(int)+0x3a) [0x2aaab4942aba]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libutility.so(utility::excn::Exception::Exception(char const*, int, std::string const&)+0x51) [0x2aaab9be84c1]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libutility.so(utility::exit(char const*, int, std::string const&, int)+0xa5) [0x2aaab9c90e85]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::AtomTreeDiffJobInputter::fill_jobs(protocols::jd2::JobsContainer&)+0xa97) [0x2aaab42781d7]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::get_job_list_from_job_inputter()+0xce) [0x2aaab428ca1e]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::init_jd()+0x169) [0x2aaab428cce9]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::JobDistributor()+0xc3) [0x2aaab4291513]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::FileSystemJobDistributor()+0x14) [0x2aaab4280f64]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::JobDistributorFactory::create_job_distributor()+0x280) [0x2aaab42924f0]

/home/export/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(protocols::jd2::JobDistributor::get_instance()+0xd4) [0x2aaab428ae54]

/share/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/bin/extract_atomtree_diffs.mpi.linuxgccrelease() [0x404927]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaabc06b545]

/share/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/bin/extract_atomtree_diffs.mpi.linuxgccrelease() [0x40503c]

 

[END_BACKTRACE]

 

[FILE]: src/protocols/jd2/AtomTreeDiffJobInputter.cc

[LINE]: 132

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: No valid input structures found for AtomTreeDiff file.

 

 

 

[END_MESSAGE]

Can anyone help me troubleshoot this?

 

Thanks!!

 

Keith

[Anonymous]

This is the input command…

/share/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/bin/extract_atomtree_diffs.mpi.linuxgccrelease -database /share/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/database/ -extra_res_fa VK5.params -s silent.out -tags $(/share/apps/rosetta3.12/rosetta_src_2020.08.61146_bundle/main/source/src/apps/public/ligand_docking/best_ifaceE.py -n 10 silent.out)

it is executed in the directory with the silent.out file 

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