I am facing SEGMENTATION FAULT error when I try to generate 10000 structures in Rosetta Homology modelling. I am running this through the Batch script. For example, when I give -out:nstruct 10000 in the flag file, it generates only 48 structures after that the job gets terminated. I have attached my batch script, flag file, Error file and the Rosettta_crash.log file here. Please, can anyone help me to find the solution to this problem?
Flag File
-run:protocol threading
-in:file:alignment ./aligned.aln
-cm:aln_format general
-frag3 ./aat000_03_05.200_v1_3.gz
-frag9 ./aat000_09_05.200_v1_3.gz
-in:file:fasta ./t000_.fasta # path to target fasta file
-in:file:fullatom
-loops:frag_sizes 9 3 1
-loops:frag_files ./aat000_09_05.200_v1_3.gz ./aat000_03_05.200_v1_3.gz none
-in:file:psipred_ss2 ./t000_.psipred_ss2
-in:file:fullatom
-out:nstruct 10
-in:file:template_pdb 4f3lb_clean.pdb
-loops:extended
-loops:build_initial
-loops:remodel quick_ccd
-loops:refine refine_ccd
-random_grow_loops_by 4
-select_best_loop_from 1
-out:file:fullatom
-out:output
-out:file:silent threaded_model.out
-out:file:silent_struct_type binary
-out:file:scorefile threaded_model.fasc
-overwrite
-database
Batch Script
#!/bin/sh
#SBATCH -N 1
#SBATCH --ntasks-per-node=48
#SBATCH --job-name=Rosetta_run
#SBATCH --error=ERROR.err
#SBATCH --output=MYJOB.out
#SBATCH --partition=small
module load rosetta/3.13
cd $SLURM_SUBMIT_DIR
mpirun -np 48 minirosetta.linuxgccrelease @flags
Error Message
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 19 with PID 2843 on node cn010 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Rosetta Crash file
I have attached this as a document in text format.
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