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Rosetta_scripts error, Got some signal... It is:6

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Rosetta_scripts error, Got some signal... It is:6

Hi there,

I was trying to run this command:


$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/ 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,


Post Situation: 
Fri, 2017-04-14 14:05

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?)

Sat, 2017-04-15 13:30