Rosetta_scripts error, Got some signal… It is:6

This topic has 3 replies, 2 voices, and was last updated 7 years, 9 months ago by Anonymous.

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- April 14, 2017 at 9:05 pm #2635
  Anonymous
  Hi there,
  
  I was trying to run this command:
```
#!/bin/bash



$ROSETTA3/bin/rosetta_scripts.linuxgccdebug 

-database $ROSETTA3_DB 

-in:file:fasta ./input_files/3j5pD.fasta 

-parser:protocol ./input_files/RosettaCM101.xml 

-nstruct 200 

-relax:minimize_bond_angles 

-relax:min_type lbfgs_armijo_nonmonotone 

-relax:jump_move true 

-relax:default_repeats 3 

-relax:dualspace 

-edensity::mapfile ./input_files/emcd101_TRPVI_chainD.mrc 

-edensity::mapreso 3.3 

-edensity::cryoem_scatterers 

-out:file:silent outCM$1.silent 

-out:path:all ./output_files/CM 

-out:suffix _101_$1 

-default_max_cycles 200 
```
  But I get the following error,
```
rosetta_scripts.linuxgccdebug: src/core/pose/Pose.cc:965: void core::pose::Pose::set_phi(utility::pointer::ReferenceCount::Size, core::Real): Assertion `( residue_type(seqpos).is_protein() || residue_type(seqpos).is_peptoid() || residue_type(seqpos).is_carbohydrate() ) || print_backtrace( "residue_type(seqpos).is_protein() || residue_type(seqpos).is_peptoid() || residue_type(seqpos).is_carbohydrate()" )' failed.

Got some signal... It is:6

Process was aborted!
```
  The command has worked for me in the past using a different sample. I have also tried it without the -relax:minimize_bond_angles option but with the same results.
  
  Thank you for the help,
  
  -Joshua
- April 15, 2017 at 8:30 pm #12283
  Anonymous
  It’s kinda hard to say exactly what’s wrong without seeing the full backtrace, but it looks like it’s an issue with your input structure.
  
  Do you have any non-protein residues in your input structure? (or in any of your templates?)
- April 15, 2017 at 8:30 pm #12804
  Anonymous
  It’s kinda hard to say exactly what’s wrong without seeing the full backtrace, but it looks like it’s an issue with your input structure.
  
  Do you have any non-protein residues in your input structure? (or in any of your templates?)
- April 15, 2017 at 8:30 pm #13325
  Anonymous
  It’s kinda hard to say exactly what’s wrong without seeing the full backtrace, but it looks like it’s an issue with your input structure.
  
  Do you have any non-protein residues in your input structure? (or in any of your templates?)
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