run_multi_step_test for make_fragments failed while running 1.submit.py...Aborting!
Running 1.submit.py...
Command line: cd /home/benchmark/working_dir && unset __PYVENV_LAUNCHER__ && . /home/benchmark/prefix/nobu-5/ubuntu/python_virtual_environments/python-3.6/0914a7459116d39a620714a07fe295ba/bin/activate && python 1.submit.py
Loaded variables from 0.compile.output.json: dict_keys(['build_command_line', 'output', 'res'])
FRAG DB PREFIX /home/benchmark/prefix/fdbft
Install for MiniConda is detected, skipping installation procedure...
Updating conda base...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda update --all --yes
Channels:
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
Solving environment: / - done
# All requested packages already installed.
Setting up Conda for Python-2.7 virtual environment...
cd /home/benchmark/working_dir && unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && ( conda create --quiet --yes --prefix /home/benchmark/working_dir/.conda-python-2.7 python=2.7 || ( conda clean --yes && conda create --quiet --yes --prefix /home/benchmark/working_dir/.conda-python-2.7 python=2.7 ) )
Channels:
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/benchmark/working_dir/.conda-python-2.7
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
ca-certificates pkgs/main/linux-64::ca-certificates-2024.12.31-h06a4308_0
certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
pip pkgs/main/linux-64::pip-19.3.1-py27_0
python pkgs/main/linux-64::python-2.7.18-h42bf7aa_3
readline pkgs/main/linux-64::readline-8.2-h5eee18b_0
setuptools pkgs/main/linux-64::setuptools-44.0.0-py27_0
sqlite pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0
tk pkgs/main/linux-64::tk-8.6.14-h39e8969_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Getting python configuration info...
unset __PYVENV_LAUNCHER__ && cd /home/benchmark/working_dir/.conda-python-2.7/bin && PATH=.:$PATH && /home/benchmark/working_dir/.conda-python-2.7/bin/python2.7 /home/benchmark/working_dir/.conda-python-2.7/bin/python2.7-config --prefix --includes
/home/benchmark/working_dir/.conda-python-2.7
-I/home/benchmark/working_dir/.conda-python-2.7/include/python2.7 -I/home/benchmark/working_dir/.conda-python-2.7/include/python2.7
Adding extra extra channel bioconda...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && conda config --env --add channels bioconda
Adding extra extra channel compbiocore...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && conda config --env --add channels compbiocore
Setting up extra packages perl perl-if perl-parallel-forkmanager perl-switch perl-text-balanced perl-json...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && conda install --quiet --yes perl perl-if perl-parallel-forkmanager perl-switch perl-text-balanced perl-json
Channels:
- compbiocore
- bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/benchmark/working_dir/.conda-python-2.7
added / updated specs:
- perl
- perl-if
- perl-json
- perl-parallel-forkmanager
- perl-switch
- perl-text-balanced
The following NEW packages will be INSTALLED:
perl pkgs/main/linux-64::perl-5.38.2-0_h5eee18b_perl5
perl-common-sense compbiocore/linux-64::perl-common-sense-3.74-pl526_1
perl-if compbiocore/linux-64::perl-if-0.0608-pl526_1
perl-json compbiocore/linux-64::perl-json-2.90-pl526_1
perl-json-xs compbiocore/linux-64::perl-json-xs-2.34-pl526_1
perl-parallel-for~ compbiocore/linux-64::perl-parallel-forkmanager-1.17-pl526_1
perl-switch compbiocore/linux-64::perl-switch-2.17-pl526_1
perl-text-balanced compbiocore/linux-64::perl-text-balanced-2.03-pl526_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Checking for frag_db...
True or != make_fragments benchmark v1.0 installed June 11 2019 -- rebuilding database
Installing dependencies...
cd /home/benchmark/prefix/fdbft && unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && export LOCAL_NR_COPY=/home/benchmark/fragment_picking_database && ./install_dependencies.pl standard localnrcopy && cd /home/benchmark/working_dir
Installed
blast: /home/benchmark/prefix/fdbft/blast
psipred: /home/benchmark/prefix/fdbft/psipred
csblast: /home/benchmark/prefix/fdbft/csblast
sparks-x: /home/benchmark/prefix/fdbft/sparks-x
nr_pfilt: /home/benchmark/prefix/fdbft/databases/nr_pfilt
Done!
>>>> PLEASE CITE THE FOLLOWING FOR BLAST <<<<
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller
W. & Lipman, D.J (1997) "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs." Nucleic Acids Res. 25:3389-3402.
>>>> PLEASE CITE THE FOLLOWING FOR PSIPRED <<<<
Jones, D.T. (1999) Protein secondary structure prediction based on
position-specific scoring matrices. J. Mol. Biol. 292:195-202.
>>>> PLEASE CITE THE FOLLOWING FOR CSBLAST <<<<
Angermüller, C., Biegert, A., & Söding, J. (2012). Discriminative modelling of
context-specific amino acid substitution probabilities. Bioinformatics, 28(24),
3240-3247.
Biegert, A., & Söding, J. (2009). Sequence context-specific profiles for
homology searching. Proceedings of the National Academy of Sciences,106(10),
3770-3775.
>>>> PLEASE CITE THE FOLLOWING FOR SPARKS-X <<<<
Y. Yang, E. Faraggi, H. Zhao and Y. Zhou. Improving protein fold recognition
and template-based modeling by employing probabilistic-based matching between
predicted one-dimensional structural properties of the query and corresponding
native properties of templates. Bioinformatics 27, 2076-2082 (2011)
FOR ACADEMIC USE ONLY.
Running test-make_fragments.pl...
cd /tmp/tmp7p1is_r6 && unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && export ROSETTA_DATABASE=/home/benchmark/rosetta/database && export VALL=/home/benchmark/rosetta/tools/fragment_tools/vall.jul19.2011 && export FRAGMENT_PICKER=/home/benchmark/rosetta/source/bin/fragment_picker.mpi.linuxgccrelease && export FRAGMENT_PICKER_NUM_CPUS=1 && export BLAST_NUM_CPUS=6 && export PERL5LIB=/home/benchmark/working_dir/.conda-python-2.7/lib/site_perl/5.26.2/ && /home/benchmark/prefix/fdbft/make_fragments.pl -n_frags 200 -frag_sizes 3,9 1a19.fasta
Use of uninitialized value $ENV{"PSIPRED_USE_weights_dat4"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 51.
Use of uninitialized value $ENV{"SLAVE_LAUNCHER_MAX_JOBS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 70.
Use of uninitialized value $ENV{"SLAVE_MAX_WAIT"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 72.
Use of uninitialized value $ENV{"SLAVE_MAX_ATTEMPTS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 73.
Use of uninitialized value $ENV{"PDB2VALL_IGNORE_ERRORS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 79.
File for psipred not found! Generating from scratch instead.
picking fragments with options:
add_pdbs_to_vall:
chain: _
cleanup: 1
csbuild_profile: 0
exclude_homologs_by_pdb_date: 0
f: 1a19.fasta
fastafile: t001_.fasta
frag_sizes: 3,9
frags: 1
homs: 1
id: t001
n_candidates: 1000
n_frags: 200
old_name_format: 0
porter: 0
porterfile:
psipred: 1
psipredfile:
rundir: /tmp/tmp7p1is_r6
runid: t001_
sam: 0
samfile:
torsion_bin: 0
--------------------------------------------------------------------------------
running psiblast for sequence: t001_.fasta
[blastpgp] WARNING: a standard checkpoint file should have extension ".chk".
[nobu-5:2023104] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 582
[nobu-5:2023104] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 166
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[nobu-5:2023104] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
Error: expected creation of t001_.200.3mers after running '/home/benchmark/rosetta/source/bin/fragment_picker.mpi.linuxgccrelease @t001__picker_cmd_size3.txt -j 1 -multithreading:total_threads 1'!
Encounter error while executing: cd /tmp/tmp7p1is_r6 && unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && export ROSETTA_DATABASE=/home/benchmark/rosetta/database && export VALL=/home/benchmark/rosetta/tools/fragment_tools/vall.jul19.2011 && export FRAGMENT_PICKER=/home/benchmark/rosetta/source/bin/fragment_picker.mpi.linuxgccrelease && export FRAGMENT_PICKER_NUM_CPUS=1 && export BLAST_NUM_CPUS=6 && export PERL5LIB=/home/benchmark/working_dir/.conda-python-2.7/lib/site_perl/5.26.2/ && /home/benchmark/prefix/fdbft/make_fragments.pl -n_frags 200 -frag_sizes 3,9 1a19.fasta
Encounter error while executing: cd /tmp/tmp7p1is_r6 && unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && export ROSETTA_DATABASE=/home/benchmark/rosetta/database && export VALL=/home/benchmark/rosetta/tools/fragment_tools/vall.jul19.2011 && export FRAGMENT_PICKER=/home/benchmark/rosetta/source/bin/fragment_picker.mpi.linuxgccrelease && export FRAGMENT_PICKER_NUM_CPUS=1 && export BLAST_NUM_CPUS=6 && export PERL5LIB=/home/benchmark/working_dir/.conda-python-2.7/lib/site_perl/5.26.2/ && /home/benchmark/prefix/fdbft/make_fragments.pl -n_frags 200 -frag_sizes 3,9 1a19.fasta
Use of uninitialized value $ENV{"PSIPRED_USE_weights_dat4"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 51.
Use of uninitialized value $ENV{"SLAVE_LAUNCHER_MAX_JOBS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 70.
Use of uninitialized value $ENV{"SLAVE_MAX_WAIT"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 72.
Use of uninitialized value $ENV{"SLAVE_MAX_ATTEMPTS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 73.
Use of uninitialized value $ENV{"PDB2VALL_IGNORE_ERRORS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 79.
File for psipred not found! Generating from scratch instead.
picking fragments with options:
add_pdbs_to_vall:
chain: _
cleanup: 1
csbuild_profile: 0
exclude_homologs_by_pdb_date: 0
f: 1a19.fasta
fastafile: t001_.fasta
frag_sizes: 3,9
frags: 1
homs: 1
id: t001
n_candidates: 1000
n_frags: 200
old_name_format: 0
porter: 0
porterfile:
psipred: 1
psipredfile:
rundir: /tmp/tmp7p1is_r6
runid: t001_
sam: 0
samfile:
torsion_bin: 0
--------------------------------------------------------------------------------
running psiblast for sequence: t001_.fasta
[blastpgp] WARNING: a standard checkpoint file should have extension ".chk".
[nobu-5:2023104] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 582
[nobu-5:2023104] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 166
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[nobu-5:2023104] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
Error: expected creation of t001_.200.3mers after running '/home/benchmark/rosetta/source/bin/fragment_picker.mpi.linuxgccrelease @t001__picker_cmd_size3.txt -j 1 -multithreading:total_threads 1'!
Traceback (most recent call last):
File "1.submit.py", line 144, in <module>
(f'cd {tmpdir}'
File "/home/benchmark/rosetta/tests/scientific/tests/make_fragments/benchmark/tests/__init__.py", line 277, in execute
raise BenchmarkError('\nEncounter error while executing: ' + command_line + '\n' + output)
benchmark.tests.BenchmarkError:
Encounter error while executing: cd /tmp/tmp7p1is_r6 && unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/ubuntu/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && export ROSETTA_DATABASE=/home/benchmark/rosetta/database && export VALL=/home/benchmark/rosetta/tools/fragment_tools/vall.jul19.2011 && export FRAGMENT_PICKER=/home/benchmark/rosetta/source/bin/fragment_picker.mpi.linuxgccrelease && export FRAGMENT_PICKER_NUM_CPUS=1 && export BLAST_NUM_CPUS=6 && export PERL5LIB=/home/benchmark/working_dir/.conda-python-2.7/lib/site_perl/5.26.2/ && /home/benchmark/prefix/fdbft/make_fragments.pl -n_frags 200 -frag_sizes 3,9 1a19.fasta
Use of uninitialized value $ENV{"PSIPRED_USE_weights_dat4"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 51.
Use of uninitialized value $ENV{"SLAVE_LAUNCHER_MAX_JOBS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 70.
Use of uninitialized value $ENV{"SLAVE_MAX_WAIT"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 72.
Use of uninitialized value $ENV{"SLAVE_MAX_ATTEMPTS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 73.
Use of uninitialized value $ENV{"PDB2VALL_IGNORE_ERRORS"} in int at /home/benchmark/prefix/fdbft/make_fragments.pl line 79.
File for psipred not found! Generating from scratch instead.
picking fragments with options:
add_pdbs_to_vall:
chain: _
cleanup: 1
csbuild_profile: 0
exclude_homologs_by_pdb_date: 0
f: 1a19.fasta
fastafile: t001_.fasta
frag_sizes: 3,9
frags: 1
homs: 1
id: t001
n_candidates: 1000
n_frags: 200
old_name_format: 0
porter: 0
porterfile:
psipred: 1
psipredfile:
rundir: /tmp/tmp7p1is_r6
runid: t001_
sam: 0
samfile:
torsion_bin: 0
--------------------------------------------------------------------------------
running psiblast for sequence: t001_.fasta
[blastpgp] WARNING: a standard checkpoint file should have extension ".chk".
[nobu-5:2023104] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 582
[nobu-5:2023104] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 166
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[nobu-5:2023104] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
Error: expected creation of t001_.200.3mers after running '/home/benchmark/rosetta/source/bin/fragment_picker.mpi.linuxgccrelease @t001__picker_cmd_size3.txt -j 1 -multithreading:total_threads 1'!