[phenixbb] Phenix rosetta refine error

pravin.jagtap at embl.de pravin.jagtap at embl.de
Thu Feb 23 05:55:42 PST 2017


Hi All,
I want to do phenix.rosetta refinement. I was successful in compiling rosetta and build the rosetta_refine interface. However when I try to do the refinement, I get the following error. I get the similar error in Rosetta_MR. Please let me know if you need any other information.

Thanks and regards,
Pravin.
RuntimeError : Aborted due to error in job 1.
Traceback:
  File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/cctbx_project/libtbx/runtime_utils.py", line 179, in run
    return_value = self.target()

  File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__
    result = self.run()

  File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/command_line/rosetta_refine.py", line 302, in run
    return run(args=list(self.args))

  File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run
    debug=params.output.debug)

  File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__
    self.run_jobs()

  File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 397, in run_jobs
    check_result(result)

  File "/struct/jhennig/jagtap/softwares/phenix-dev-2689/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result
    raise RuntimeError("Aborted due to error in job %d." % result.job_id)
Platform info:
__FILE__ = /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos6/modules/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Feb 18 2017
__TIME__ = 00:45:46
__TIMESTAMP__ = Tue Nov  8 23:38:16 2016
__x86_64__
__linux
__GNUC__ = 4
__GNUC_MINOR__ = 4
__GNUC_PATCHLEVEL__ = 7
boost::python::cxxabi_cxa_demangle_is_broken(): false
__GXX_WEAK__ = 1
__LP64__ = 1
__VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-16)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 61
__SSE2__ = 1
BOOST_LIB_VERSION = 1_55
PY_VERSION = 2.7.8
PYTHON_API_VERSION = 1013
sizeof(bool) = 1
sizeof(short) = 2
sizeof(int) = 4
sizeof(long) = 8
sizeof(std::size_t) = 8
sizeof(void*) = 8
sizeof(long long) = 8
sizeof(float) = 4
sizeof(double) = 8
sizeof(long double) = 16
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
__PTRDIFF_TYPE__
Py_USING_UNICODE
sizeof(PY_UNICODE_TYPE) = 2
_OPENMP = 200805
gnu libc version: 2.17
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
boost/TAG: 86799
os.name: posix
sys.platform: linux2
sys.byteorder: little
platform.platform(): Linux-3.10.0-514.6.1.el7.x86_64-x86_64-with-centos-7.3.1611-Core
platform.architecture(): ('64bit', 'ELF')
floating_point_exceptions.division_by_zero_trapped: False
floating_point_exceptions.invalid_trapped: False
floating_point_exceptions.overflow_trapped: False
number of processors: 8
Memory total:  8,292,691,968
Memory free:     703,213,568
import thread: OK
"hello" = ['h', 'e', 'l', 'l', 'o']
u"hello" = ['h', 'x00', 'e', 'x00', 'l', 'x00', 'l', 'x00', 'o', 'x00']
u"u00C5" = ['xc5', 'x00'] as utf-8 = ['xc3', 'x85']
LATIN CAPITAL LETTER A WITH RING ABOVE = Å
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