Discussion group for the ARIA software

[Xiao Wang <xiao.wang AT etu.parisdescartes.fr>]

Good afternoon everbody,

I used aria 2.3.2 to calculate structure with ccpnmr project and it works well for the first time.  THen I modified a few assignment according the results of violation.

 I run the aria again, but something  is wrong. the log is:

[wangxiao@laurier ~/6labled_p6]$ aria2 --setup 29062020.xml

ARIA Version 2.3.2. 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 "29062020.xml"...
Setting-up 29062020.xml (run: Hiv_p6_29062020)
WARNING [Project]: Project path "/home/wangxiao/6labled_p6" does already exist.
MESSAGE [Project]: Protocols copied.
MESSAGE [Project]: Directory tree created.
MESSAGE [Project]: Copying data files into local data-directory...
WARNING [Project]: File "Molecule_1+11032020p6_wangxiao_2020-06-17-15-44-32-117_
                   00001.xml" for data of type "spectrum" already exists in
                   local data directory; local copy will be used.

Done.

For running ARIA: aria2 29062020.xml

[wangxiao@laurier ~/6labled_p6]$ aria2 29062020.xml

ARIA Version 2.3.2. 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 "29062020.xml"...
MESSAGE [Project]: Temporary directory has been set to /home/wangxiao/
                   6labled_p6/aria_temp.tmpZCYuYX1593439325
MESSAGE [Project]: List of available machines is empty. Running calculations on
                   localhost "laurier", assuming 1 CPU. Using /home/wangxiao/
                   PROGS/cns_solve_1.21/intel-x86_64bit-linux/bin/cns as
                   structure engine.
MESSAGE [Project]: Checking host list ...
MESSAGE [Job manager]: Command "csh -f" ... ok.
MESSAGE [Project]: Cache is disabled.
Model read finished. Duration 0.894577980042
Model validity check skipped
MESSAGE [Project]: ------------ Reading data from CCPN data model ------------
MESSAGE [Project]: Opening CCPN data model "/home/wangxiao/6labled_p6/
                   P6_PROJECT/11032020p6"...
MESSAGE [Project]: CCPN data model opened.
MESSAGE [Project]: Retrieving molecular system "MS1", chain code(s) "A"...
MESSAGE [Project]: Retrieving Constraint List "4|1" of type "dihedrals" ...
MESSAGE [Project]: Retrieving peak list "(project=HIVP6, experiment=3,
                   data_source=1, serial=1)", shift list "1" ...
WARNING [CCPN import]: Attempt to get atoms from unassigned CCPN resonance
                       (405)
Error loading file for:  <ccpnmr.NameMapping.NameMappingStore ['11032020p6']>
Reading:  <open file '/home/wangxiao/6labled_p6/P6_PROJECT/11032020p6/ccpnmr/Nam
eMapping/11032020p6+11032020p6_wangxiao_2020-06-24-15-13-00-767_00001.xml', mode
 'r' at 0x27b939c0>
Last xml tag read:  NMAP.NameMappingStore.nameMappings
Parser state was:  postprocessing data
Object stack was empty
Traceback (most recent call last):
  File "/home/wangxiao/PROGS/aria2.3//aria2.py", line 903, in <module>
    verbose_level, use_condor=condor)
  File "/home/wangxiao/PROGS/aria2.3//aria2.py", line 811, in run_aria
    project.load_and_preprocess_data()
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Project.py", line 1468, in load
_and_preprocess_data
    self.read_data()
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Project.py", line 1198, in read
_data
    self.read_ccpn_data()
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/Project.py", line 871, in read_
ccpn_data
    data_dir, cType)
  File "/home/wangxiao/PROGS/aria2.3/src/py/aria/importFromCcpn.py", line 1191,
in dumpRestraintsList
    cns_format = CnsFormat(ccpProject)
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/ccpnmr/format/converters/Da
taFormat.py", line 924, in __init__
    self.getNameMapping()
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/ccpnmr/format/general/TopSh
ared.py", line 179, in getNameMapping
    if not self.project.currentNameMappingStore:
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/memops/api/Implementation.p
y", line 16972, in getCurrentNameMappingStore
    self.findFirstNameMappingStore()
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/memops/api/Implementation.p      y", line 14505, in findFirstNameMappingStore
    root.refreshTopObjects('ccpnmr.NameMapping')
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/memops/api/Implementation.p      y", line 18244, in refreshTopObjects
    topObject = XmlIO.loadFromFile(self, filePath, partialLoad=True)
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/memops/format/xml/XmlIO.py"      , line 251, in loadFromFile
    partialLoad=partialLoad)
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/memops/format/xml/XmlIO.py"      , line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/memops/xml/Implementation.p      y", line 5333, in loadFromStream
    linkChildData(delayDataDict, result, mapping, linkTopToParent, doOutOfPackag      e)
  File "/home/wangxiao/PROGS/ccpnmr/ccpnmr2.4/python/memops/xml/Implementation.p      y", line 5540, in linkChildData
    + ": %s:%s:%s" % (obj.getQualifiedName(), obj.getParent(), key)
memops.general.Implementation.ApiError: Cannot add child - key already in use: c      cpnmr.NameMapping.NameMappingStore:<memops.Implementation.MemopsRoot id:58421070      4>:11032020p6

IS there any good suggestion? Thanks in advance.

WANG Xiao

Ph.D. Student

Paris Descartes University, Faculty of Pharmacy Therapeutic Targets and Drug Design -CiTCoM-UMR 8038

75270 Paris CEDEX 06