[phenixbb] Problem with mr_rosetta

[Kerff Fred]

Hello,

I’m trying to use mr_rosetta on my protein. I’m using OS X and upgraded phenix a couple of days ago and install rosetta at the same time.

My job stops with the following message in this log file /phenix/MR_ROSETTA_52/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_6/WORK_1/rebuild.log.

ERROR:  can't find residue type at pos 1 in sequence 
...sequence removed…

ERROR:: Exit from: src/core/pose/annotated_sequence.cc line: 236
0   mr_protocols.macosclangrelease      0x000000010b198bd6 print_backtrace() + 54
1   mr_protocols.macosclangrelease      0x000000010b198ab4 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 804
2   mr_protocols.macosclangrelease      0x000000010a9b8ca1 core::pose::residue_types_from_sequence(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::chemical::ResidueTypeSet const&, bool) + 3697
3   mr_protocols.macosclangrelease      0x000000010a9ba6ea core::pose::make_pose_from_sequence(core::pose::Pose&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, core::chemical::ResidueTypeSet const&, bool) + 26
4   mr_protocols.macosclangrelease      0x0000000109267969 protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(core::pose::Pose&, std::__1::shared_ptr<protocols::jd2::Job>) + 1449
5   mr_protocols.macosclangrelease      0x0000000109cb0c58 protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, unsigned long&, unsigned long&, bool) + 2232
6   mr_protocols.macosclangrelease      0x0000000109cafb5b protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 331
7   mr_protocols.macosclangrelease      0x0000000109c8d1f2 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66
8   mr_protocols.macosclangrelease      0x00000001089e9964 my_main(void*) + 3124
9   mr_protocols.macosclangrelease      0x00000001089eae19 main + 4713
10  libdyld.dylib                       0x00007fff8c8555c9 start + 1
11  ???                                 0x0000000000000002 0x0 + 2
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job 'S_PHENI_0001'
Error: 

[ERROR] EXCN_utility_exit has been thrown from: src/core/pose/annotated_sequence.cc line: 236
ERROR:  can't find residue type at pos 1 in sequence 
...sequence removed...


Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: S_PHENI_0001
protocols.jd2.JobDistributor: no more batches to process... 
protocols.jd2.JobDistributor: 15 jobs considered, 1 jobs attempted in 0 seconds
caught exception 1 jobs failed; check output for error messages


Anybody can help?

Thanks

Fred
-----
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000 Liège (Belgium)
Tel.: +32 (0)4 3663620
Fax: +32 (0)4 3663772



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