0000095: AbinitioRelax crashes if given fasta file for short peptide (6 residues confirmed to fail)

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0000095

Rosetta

[All Projects] Crash

public

2012-09-05 09:41

2012-09-05 10:50

Reporter

smlewis

Assigned To

smlewis

Priority

normal

Severity

major

Reproducibility

always

Status

resolved

Resolution

fixed

Platform

OS Version

Product Version

Fixed in Version

Trunk

Summary

0000095: AbinitioRelax crashes if given fasta file for short peptide (6 residues confirmed to fail)

Description

http://www.rosettacommons.org/content/abinitiorelax-very-small-peptides [^]

Briefly, if you try to run abrelax on a short peptide (I am guessing shorter than 9, but 6 is confirmed to fail), abrelax crashes.

Additional Information

Error at standard verbosity:

***************************************
core.init: Mini-Rosetta version unknown from unknown
core.init: command: ./AbinitioRelax.default.linuxgccrelease @AbFlags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1128871718 seed_offset=0 real_seed=-1128871718
core.init.random: RandomGenerator:init: Normal mode, seed=-1128871718 RG_type=mt19937
protocols.abinitio.AbrelaxApplication: read fasta sequence: 6 residues
LRPWYR
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1980 residue types

ERROR: seqpos <= size()
ERROR:: Exit from: src/core/conformation/Conformation.hh line: 289
**********************************************

Error at super-verbosity (just the end bit):

core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1980 residue types
core.pose: one_letter: LRPWYR
core.pose: seq_in: LRPWYR
core.pose: residue_types_from_sequence(): seqpos: 1 aa L LEU
core.pose: residue_types_from_sequence(): seqpos: 2 aa R ARG
core.pose: residue_types_from_sequence(): seqpos: 3 aa P PRO
core.pose: residue_types_from_sequence(): seqpos: 4 aa W TRP
core.pose: residue_types_from_sequence(): seqpos: 5 aa Y TYR
core.pose: residue_types_from_sequence(): seqpos: 6 aa R ARG
core.pose: make_pose_from_sequence(): seqpos: 1 LEU
core.pose: make_pose_from_sequence(): seqpos: 2 ARG
core.pose: make_pose_from_sequence(): seqpos: 3 PRO
core.pose: make_pose_from_sequence(): seqpos: 4 TRP
core.pose: make_pose_from_sequence(): seqpos: 5 TYR
core.pose: make_pose_from_sequence(): seqpos: 6 ARG
core.pose: sequence in pose: LRPWYR
core.pose: annotated seq: L[LEU_p:NtermProteinFull]RPWYR[ARG_p:CtermProteinFull]

ERROR: seqpos <= size()
ERROR:: Exit from: src/core/conformation/Conformation.hh line: 289

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Application(s) Affected

AbinitioRelax

Command Line Used

reported at top of forum thread

Developer Options

Confirmed As Bug

Fixed in SVN Version

50962

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Notes
(0000092) smlewis (Administrator) 2012-09-05 10:50	Someone left weird debugging code in AbrelaxApplication.cc: 1128 tr.Debug << "CHECK PHI/PSI/OMEGA pos 8: " << extended_pose.phi( 8 ) << " " 1129 << extended_pose.psi( 8 ) << " " << extended_pose.omega( 8 ) 1130 << std::endl; hardcoded references to residue 8 cause failures for shorter poses, of course.

Issue History
Date Modified	Username	Field	Change
2012-09-05 09:41	smlewis	New Issue
2012-09-05 10:50	smlewis	Fixed in SVN Version	=> 50962
2012-09-05 10:50	smlewis	Note Added: 0000092
2012-09-05 10:50	smlewis	Status	new => resolved
2012-09-05 10:50	smlewis	Fixed in Version	=> Trunk
2012-09-05 10:50	smlewis	Resolution	open => fixed
2012-09-05 10:50	smlewis	Assigned To	=> smlewis