Segmentation fault (core dumped) denovo_density.linuxgccrelease

[Anonymous]

I’m trying to run the below script, I’m getting a lot of lines liek the following. I would appreciate your help with that. Thanks. 

 

./tubulin_fragment_search_iteration.sh: line 23: 22106 Segmentation fault      (core dumped) $ROSETTA3/source/bin/denovo_density.linuxgccrelease -in::file::fasta /home/labusr/Desktop/chlamy_paper/pacrg_fap20.fasta -fragfile /home/labusr/Desktop/chlamy_paper/pacrg_fap20_9mer -mapfile /home/labusr/Desktop/chlamy_paper/PACRG_FAP20_8nmmap_4_4angstrome_res_one_unit.mrc -n_to_search 1000 -n_filtered 4500 -n_output 50 -bw 16 -atom_mask_min 2 -atom_mask 3 -clust_radius 3 -clust_oversample 4 -point_radius 3 -movestep 1 -delR 2 -frag_dens 0.8 -ncyc 3 -min_bb false -pos $1 -out:file:silent round1_pacrg_fap20/pacrg_fap20.$1.silent

 

#!/bin/sh





mkdir -p round1_pacrg_fap20



$ROSETTA3/source/bin/denovo_density.linuxgccrelease

-in::file::fasta /home/labusr/Desktop/chlamy_paper/pacrg_fap20.fasta

-fragfile /home/labusr/Desktop/chlamy_paper/pacrg_fap20_9mer

-mapfile /home/labusr/Desktop/chlamy_paper/PACRG_FAP20_8nmmap_4_4angstrome_res_one_unit.mrc

-n_to_search 1000 -n_filtered 4500 -n_output 50 

-bw 16 

-atom_mask_min 2 

-atom_mask 3 

-clust_radius 3 

-clust_oversample 4 

-point_radius 3 

-movestep 1 

-delR 2 

-frag_dens 0.8 

-ncyc 3 

-min_bb false 

-pos $1 

-out:file:silent round1_pacrg_fap20/pacrg_fap20.$1.silent

 

 

[Anonymous]

This isn’t enough log to tell us anything unfortunately.  Standard advice for segfaults applies: re-run in debug mode, possibly also with -out:level 500, and then let’s see what’s at the end of the log file.  Be sure to run straight in terminal, not piped into a file, since that will eat the last log chunk when it crashes.

[Author]

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