Rosetta Antibody: Unable to open file and terminates

[Anonymous]

Hello, please note I’m revising my posting with some major updates, apologies to the 9 viewers who have come here prior as this will read completely different.

 

I’m encountering a read error with antibody_H3. Below is the executable I ran (I’ve also reproduced the error with .static mode):

mpiexec -np 4 $ROSETTA3/bin/antibody_H3.cxx11threadmpiserialization.linuxgccrelease 

@abH3.flags

abH3.flags looks just like:

# input grafted model

-s experiment1/model-0.relaxed.pdb



# recommended number of structs

-nstruct 100



# enable contraints (probably should just detect weight in future)

-antibody:constrain_cter

-constraints:cst_weight 1.0



# recommended kink cst, kink present in 90% of Abs

-antibody:auto_generate_kink_constraint

-antibody:all_atom_mode_kink_constraint



# recommended VH-VL Q-Q constraint, you must manually specify the file (see integration test)

-antibody:constrain_vlvh_qq



# standard settings, for packages used by antibody_H3

-ex1

-ex2

-extrachi_cutoff 0



# necessary if running multiple procs w/o MPI

-multiple_processes_writing_to_one_directory



# specify output file

-out:file:scorefile H3_modeling_scores.fasc



# specify output folder

-out:path:pdb experiment1/H3_modeling 

 

Error message:

protocols.jd2.MPIWorkPoolJobDistributor: (1) {0} Slave Node 1: Finished job successfully! Sending output request to master.

protocols.jd2.MPIWorkPoolJobDistributor: (0) {0} Master Node: Received message from  1 with tag 30

protocols.jd2.MPIWorkPoolJobDistributor: (0) {0} Master Node: Received job success message for job id 1 from node 1 blocking till output is done

protocols.jd2.MPIWorkPoolJobDistributor: (1) {0} Slave Node 1: Received output confirmation from master. Writing output.



ERROR: Unable to open file: ~/experiment1/H3_modeling/model-0.relaxed_0001.pdb



ERROR:: Exit from: src/protocols/jd2/wwPDBJobOutputter.cc line: 89



[ ERROR ]: Caught exception:





File: src/protocols/jd2/wwPDBJobOutputter.cc:89

[ ERROR ] UtilityExitException

ERROR: Unable to open file: ~/experiment1/H3_modeling/model-0.relaxed_0001.pdb











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





Primary job  terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.



mpiexec detected that one or more processes exited with non-zero status, thus causing

the job to be terminated. The first process to do so was:



Process name: [[21298,1],1]

Exit code:    255

 

ROSETTA_CRASH.log:

#

# Rosetta crash log.

#



[START_CRASH_REPORT]

[ROSETTA_VERSION]: 2019.35+release.767c1ea

[COMMIT_DATE]: 2019-08-30T12:04:30.133343

[APPLICATION]: /home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_H3.cxx11threadmpiserialization.linuxgccrelease

[MODE]: Release

[EXTRAS]: cxx11thread mpi (OpenMPI 2.1.1) serialization

[OS]: GNU/Linux

[COMPILER]: GCC version "7.4.0"

[STDLIB]: libstdc++ version 20181206

[START_OPTIONS]

-in:file:s=experiment1/model-0.relaxed.pdb -out:nstruct=1 -out:file:scorefile=H3_modeling_scores.fasc -out:path:pdb=~/experiment1/H3_modeling/ -run:multiple_processes_writing_to_one_directory -packing:extrachi_cutoff=0 -packing:ex1 -packing:ex2 -constraints:cst_weight=1 -antibody:constrain_cter -antibody:constrain_vlvh_qq -antibody:auto_generate_kink_constraint -antibody:all_atom_mode_kink_constraint



[END_OPTIONS]



[START_BACKTRACE]: RAW_LIBC

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libutility.so(backtrace_string[abi:cxx11](int)+0x56) [0x7fa52535d576]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe3) [0x7fa52535cba3]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x10f) [0x7fa525414aff]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x36) [0x7fa5254148b6]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libprotocols.1.so(protocols::jd2::wwPDBJobOutputter::final_pose(std::shared_ptr<protocols::jd2::Job>, core::pose::Pose const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x1b91) [0x7fa526a387a1]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libprotocols.1.so(protocols::jd2::MPIWorkPoolJobDistributor::slave_job_succeeded(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x3f5) [0x7fa5269db795]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libprotocols.1.so(protocols::jd2::MPIWorkPoolJobDistributor::job_succeeded(core::pose::Pose&, double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x29) [0x7fa5269d4f49]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libprotocols.1.so(protocols::jd2::JobDistributor::write_output_from_job(core::pose::Pose&, std::shared_ptr<protocols::moves::Mover>, protocols::moves::MoverStatus, unsigned long, unsigned long&)+0xc08) [0x7fa52698e8b8]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe63) [0x7fa52698fb13]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x176) [0x7fa526991956]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-serialization/libprotocols.1.so(protocols::jd2::MPIWorkPoolJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x3bc) [0x7fa5269dc26c]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_H3.cxx11threadmpiserialization.linuxgccrelease(+0xbd05) [0x5644008edd05]

/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7fa524109b97]

/home/baverso/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_H3.cxx11threadmpiserialization.linuxgccrelease(+0xbf2a) [0x5644008edf2a]



[END_BACKTRACE]



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

[LINE]: 89

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: Unable to open file: ~/experiment1/H3_modeling/model-0.relaxed_0001.pdb









[END_MESSAGE]

[END_CRASH_REPORT]

 

 

 

The file it’s trying to open is one that the executable generates in the process of compiling. Any advice on how I could resolve this bug? Thanks so much for any advice.

 

Versioning / Machine specs:

Rosetta 3.11, Ubuntu 18.04. Package specs attached to this post.

 

[Anonymous]

Update: I’ve resolved the problem. The abH3.flags parameter -out:path:pdb experiment1/H3_modeling  was originally specified with the full path ~/experiment1/H3_modeling which for some reason did not agree with its functionality. Marking resolved!

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