Gajoe run on external pool

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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vas2201
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Joined: 2018.08.13 23:27

Gajoe run on external pool

#1 Post by vas2201 » 2018.09.13 00:45

I am trying to run gajoe module on pool from MD simulation using shell script, I am getting the following error. But if ran it the terminal command ( gajoe -p ), it was working fine. .

I want to give the default parameters as input file and running gajoe -p < input file. I am getting segmentation fault error and sh: /usr/bin/ls: Argument list too long.


selectEnsemble.sh script

#!/bin/bash
# select the ensemble by EOM

#gajoe13 < input/eo.in
source ~/.bashrc
module load ATSAS
gajoe -p < /home/srp106/Desktop/SAXS-ER-1.1/SAXS-ER/SAXS-ER/aMD-2.1/input/gajoe.in


output and errors
[srp106@gput026 aMD-2.1]$ gajoe -p < /home/srp106/Desktop/SAXS-ER-1.1/SAXS-ER/SAXS-ER/aMD-2.1/input/gajoe.in
******* ------------------------------------------------------ *******
******* GAJOE - version 2.1 - (r4556) *******
******* Copyright (c) ATSAS Team *******
******* EMBL, Hamburg Outstation, 2007 - 2014 *******
******* *******
******* For doubts/questions please visit SAXIER forum: *******
******* http://www.saxier.org/forum/viewforum.php?f=10 *******
******* *******
******* In case of bugs please refer to: *******
******* G. Tria, D.I. Svergun, EMBL BioSAXS group *******
******* atsas@embl-hamburg.de *******
******* ------------------------------------------------------ *******
---------------------------- ATTENTION ------------------------------
Using a pool of PDBs could take a while due to the CRYSOL computation
---------------------------------------------------------------------
Number of experimental curves to fit? (default: 1) ................... : Experimental data file name 1? (*.dat) .............................. : Directory containing the PDB files? (default: .) ..................... : Number of harmonics (min. 10, max. 50)? (default: 15) ................ : Maximum s value (min. 0.1, max. 0.5)? (default: 0.500) ............... : Number of points (min. 10, max. 201)? (default: 51) .................. : Number of generations (min. 10) (default: 1000) ...................... : Number of ensembles (min. 10) (default: 50) .......................... : Ensemble size fixed? (default: no) ................................... : Maximum number of curves per ensemble (min. 1, max. 50) (default: 20) : Minimum number of curves per ensemble (min. 1) (default: 5) .......... : Curve repetition in the ensemble allowed? (default: yes) ............. : Constant subtraction allowed? (default: yes) ......................... : Number of times you want the genetic algorithm repeated (min. 1)
(default: 100) ....................................................... : Curve: RNA_1.dat - Loading values and configuration ...
... Theoretical scattering computation (CRYSOL time) ...
sh: /usr/bin/ls: Argument list too long
[ 1%]
... CRYSOL time completed!
Number of theoretical curves : 0
Starting the Genetic Algorithm ...
Segmentation fault (core dumped)



Could you please suggest me needful?

Thanking you !

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