Dear CCPN Team ,
Structure calculation failed when increase the number of iterations 20 to 200 . what could be possible error in my input files ! I tried on my own server aria 2.2 , it is also failed . i.e it is not showing any error message and not starting run1 . i attached log here below .
what could be the possible error ?
run name : sine3
username:sri2201
Regards
Srinivas P
----------scriptsError.log----------
----------scriptsOut.log----------
found_ccpnDir sine: status 0
found_aria_file inputAria.xml: status 0
parse_prj: status 0
_open_toRunAria_
PID = 319
_parameters_
command: ['round=0', 'switch_log=1', 'input_aria=1', 'molecule=MS1|A|B', "spectra=[('sine|1|1|3 2dnoesymerge.list sparky ARIA2_NOE_Peaks_run1_it8_sine|1|1|1 intensity', 'sine|2 shifts11112.list'), ('sine|2|1|3 n15enoesy.peaks sparky ARIA2_NOE_Peaks_run1_it8_sine|2|1|1 intensity', 'sine|2 shifts11112.list')]", "hbonds=['1|2 hBond constraint list', '1|1 hBond constraint list']", "dihedrals=['1|3 dihedral constraint list', '1|4 dihedral constraint list']", "distances=['3|1 ARIA2_run1_NOEs_it8']", 'rdcs=[]', [log in to unmask], 'CONDOR=1', 'aria_xml=0', 'use_logHarm=1']
MESSAGE [ProjectXMLPickler]: No symmetry data specified. Symmetry will be
disabled.
user_aria_input_file: status 0
import_par: status 0
run_aria_pre: status 0
==========> using CONDOR
run_aria_main: status 256
job_failed: status 0
email_sent_to: sri2201 - status 0
removed_unnecessary_files '*.bak': status 0
removed_unnecessary_files 'aria_temp.tmp*': status 256
Total Running Time: 0:29:37.279868s
DONE
----------ariaOut.log----------
ARIA Version 2.3.1. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
If you use this software, please quote the following reference(s):
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382
Loading project "inputAria.xml"...
Setting-up inputAria.xml (run: 1)
WARNING [Project]: Project path "/tmp/ccpn/webapps_outputs/grid/sri2201_20120221
T093201" does already exist.
MESSAGE [Project]: Protocols copied.
MESSAGE [Project]: Directory tree created.
MESSAGE [Project]: Copying data files into local data-directory...
Done.
For running ARIA: aria2 inputAria.xml
ARIA Version 2.3.1. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
...
...
...
...[SKIP]...
...
...
...
329816846/run_cns_53/refine.csh &" completed.
MESSAGE [Job]: Job "cd /tmp/ccpn/webapps_outputs/grid/sri2201_20120221T093201/
aria_temp.tmpkTWJ5f1329816846/run_cns_112; csh -f /tmp/ccpn/
webapps_outputs/grid/sri2201_20120221T093201/aria_temp.tmpkTWJ5f1
329816846/run_cns_112/refine.csh &" completed.
MESSAGE [Job]: Job "cd /tmp/ccpn/webapps_outputs/grid/sri2201_20120221T093201/
aria_temp.tmpkTWJ5f1329816846/run_cns_42; csh -f /tmp/ccpn/
webapps_outputs/grid/sri2201_20120221T093201/aria_temp.tmpkTWJ5f1
329816846/run_cns_42/refine.csh &" completed.
MESSAGE [Job]: Job "cd /tmp/ccpn/webapps_outputs/grid/sri2201_20120221T093201/
aria_temp.tmpkTWJ5f1329816846/run_cns_111; csh -f /tmp/ccpn/
webapps_outputs/grid/sri2201_20120221T093201/aria_temp.tmpkTWJ5f1
329816846/run_cns_111/refine.csh &" completed.
MESSAGE [Job]: Job "cd /tmp/ccpn/webapps_outputs/grid/sri2201_20120221T093201/
aria_temp.tmpkTWJ5f1329816846/run_cns_108; csh -f /tmp/ccpn/
webapps_outputs/grid/sri2201_20120221T093201/aria_temp.tmpkTWJ5f1
329816846/run_cns_108/refine.csh &" completed.
MESSAGE [Job]: Job "cd /tmp/ccpn/webapps_outputs/grid/sri2201_20120221T093201/
aria_temp.tmpkTWJ5f1329816846/run_cns_30; csh -f /tmp/ccpn/
webapps_outputs/grid/sri2201_20120221T093201/aria_temp.tmpkTWJ5f1
329816846/run_cns_30/refine.csh &" completed.
MESSAGE [Job]: Job "cd /tmp/ccpn/webapps_outputs/grid/sri2201_20120221T093201/
aria_temp.tmpkTWJ5f1329816846/run_cns_101; csh -f /tmp/ccpn/
webapps_outputs/grid/sri2201_20120221T093201/aria_temp.tmpkTWJ5f1
329816846/run_cns_101/refine.csh &" completed.
MESSAGE [CNS]: CNS output files have been copied to /tmp/ccpn/webapps_outputs/
grid/sri2201_20120221T093201/run1/structures/it0/cns
MESSAGE [Job manager]: shutdown.
Traceback (most recent call last):
File "/usr/local/aria2.3/aria2.py", line 903, in
verbose_level, use_condor=condor)
File "/usr/local/aria2.3/aria2.py", line 813, in run_aria
project.go(use_condor)
File "/usr/local/aria2.3/src/py/aria/Project.py", line 1574, in go
self.run_protocol(first_iteration)
File "/usr/local/aria2.3/src/py/aria/Project.py", line 1580, in run_protocol
last_iteration = self.getProtocol().go(iteration, self.getMolecule())
File "/usr/local/aria2.3/src/py/aria/Protocol.py", line 1742, in go
iteration = self.start(iteration, molecule)
File "/usr/local/aria2.3/src/py/aria/Protocol.py", line 1726, in start
return self.run_protocol(molecule, iteration)
File "/usr/local/aria2.3/src/py/aria/Protocol.py", line 2211, in run_protocol
is_first_it)
File "/usr/local/aria2.3/src/py/aria/Protocol.py", line 2166, in run_iteration
self.error(StandardError, err_msg)
File "/usr/local/aria2.3/src/py/aria/ariabase.py", line 211, in error
raise exception, msg
StandardError: USER ERROR File "/usr/local/aria2.3/src/py/aria/Protocol.py", line 2211 in run_protocol
Structure calculation failed for structure 89.
Please check your setup and the CNS output files for errors
|