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FARFAR2 error: no edge found that contains seqpos!

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FARFAR2 error: no edge found that contains seqpos!
#1
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Hi,

I am running MPI version of rna_denovo using command below using PDB, sequence, and secondary structure as inputs :

rna_denovo.mpi.linuxgccrelease -fasta rna_sequence.fasta -secstruct_general_file rna.secstruct -native 2CKY_1.pdb -align_pdb 2CKY_1.pdb -rmsd_screen 4.0 -cycles 20000 -minimize_rna true -nstruct 100 -out:file:silent FARFAR2_native_2CKY_1.out -use_legacy_job_distributor

However, this job is failed with no edge error as mentioned in ROSETTA_CRASH.log:

###################################

[FILE]: src/core/kinematics/FoldTree.cc
[LINE]: 2353
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: no edge found that contains seqpos!

#####################################

I could not trace origin of this error. Any suggestions to understand and solve this error would be of great help.

Thanks,

Mandar

Category: 
Nucleic Acids
Post Situation: 
Unsolved
Tue, 2024-06-18 18:39
mandar
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Impossible to say for sure without your inputs, but the most common issue is with your secondary structure. It also looks like you're providing -secstruct_general without -secstruct, which is uncommon -- consider providing both?

Wed, 2024-06-19 15:21
everyday847
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We're updating the site, and as part of that we're moving the forums to Github Discussions.

If you still have questions or are still having issues, please feel free to open up a thread over there.

Thu, 2024-06-20 13:13
rmoretti