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Segmentation Fault in Rosetta CM Hybridize

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Segmentation Fault in Rosetta CM Hybridize


I'm  trying to do CM hybridize. However, there is a segmentation fault when I start to run:

[ROSETTA_VERSION]: 2020.08+release.cb1caba
[COMMIT_DATE]: 2020-02-21T14:46:08.581859
[APPLICATION]: /mnt/c/Users/yliang/Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-16)"
[STDLIB]: libstdc++ version 20150623
 -in:file:fasta=Ca09HA.fasta -in:file:spanfile=Ca09HA.span -parser:protocol=rosetta_cm_new.xml -score:weights=stage3_rlx_membrane.wts -chemical:exclude_patches=LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm -corrections:score:use_bicubic_interpolation -membrane -membrane:no_interpolate_Mpair -membrane:Menv_penalties -optimization:default_max_cycles=200 -cm:hybridize:stage1_probability=1 -relax:jump_move -relax:minimize_bond_lengths -relax:minimize_bond_angles -relax:min_type=lbfgs_armijo_nonmonotone




[LINE]: 11
Segmentation Fault


May I know how to figure out what's wrong with my running?



Post Situation: 
Mon, 2022-06-06 17:25

The first thing to do is to double check your input files, to see if there's anything obvious which isn't quite right.

Then the standard recommendation to debugging segmentation faults is to re-run things with a version of Rosetta compiled in debug mode ("mode=debug" on the scons command line, which should result in a rosetta_scripts.linuxgccdebug executable). This turns on extra checking which (while slowing down the run) should catch more errors, or at least give more informative backtraces when it does crash.

Tue, 2022-06-07 04:56

Hi Rmoretti,

Thank you for your suggestions.

I'm quite new to this Rosetta CM.  Do you mind if I send you my input files to see if they are correct?



Tue, 2022-06-07 08:36