error during JChemSearch ( error message: null )

 

Hello,

We have running PP9.0.2 Server with chemaxon 5.11.3

During a jchemsearch on a structure table we get the following error:

null
JChem version : 5.11.3
Component collection version : 2.7.1_j62
JVM: Oracle Corporation  Java HotSpot(TM) 64-Bit Server VM  1.7.0_15
Memory:  368.0 MB maximum  368.0 MB total  349.0 MB free
OS: amd64 Linux 2.6.32-71.el6.x86_64
Exception ID: E05155320
Current input structure:
c1ccccc1
Please find detailed report in log file: "/home/accelrys/.chemaxon/logs/pp_error_2014_06_06.txt"
java.lang.NullPointerException
 at chemaxon.jchem.db.JChemSearch.printSearchInfo(JChemSearch.java:2932)
 at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2847)
 at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2489)
 at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:2207)
 at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2236)
 at chemaxon.pp.JChemSearch.search(JChemSearch.java:336)
 at chemaxon.pp.JChemSearch.onProcessBody(JChemSearch.java:303)
 at chemaxon.pp.ChemAxonComponent.onProcess(ChemAxonComponent.java:53)
 at com.scitegic.pilot.Pilot.callOnProcess(Pilot.java:331)
CComponentJavaPlugin::onProcess: Pipeline Pilot exception rethrown
-> 'JChemSearch' ('Internal ChemAxon JChemSearch'); Location: 11:0 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
-> 'JChemSearch' ('JChemSearch'); Location: 11 - error during Data Record Processing phase
CProtocolStd::onProcess: Pipeline Pilot exception rethrown
CProtocol::onProcess: Pipeline Pilot exception rethrown
CComponentRunner::CallOnProcess: exception caught, calling onFinalize before rethrow
Protocol 140422_JChem Base Insert and Search, user *******: Pipeline Pilot exception caught
Protocol 140422_JChem Base Insert and Search, user *******: Protocol failed: Pipeline Pilot error
Pipeline Pilot Server version 9.0.2

in the log fil we found:

************************************************

Error report:
Fri Jun 06 13:42:41 CDT 2014

null

JChem version : 5.11.3
Component collection version : 2.7.1_j62
JVM: Oracle Corporation  Java HotSpot(TM) 64-Bit Server VM  1.7.0_15
Memory:  368.0 MB maximum  368.0 MB total  349.0 MB free
OS: amd64 Linux 2.6.32-71.el6.x86_64
Exception ID: E05155320

Current input structure:
c1ccccc1

Stack trace:
java.lang.NullPointerException
        at chemaxon.jchem.db.JChemSearch.printSearchInfo(JChemSearch.java:2932)
        at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2847)
        at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2489)
        at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:2207)
        at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2236)
        at chemaxon.pp.JChemSearch.search(JChemSearch.java:336)
        at chemaxon.pp.JChemSearch.onProcessBody(JChemSearch.java:303)
        at chemaxon.pp.ChemAxonComponent.onProcess(ChemAxonComponent.java:53)
        at com.scitegic.pilot.Pilot.callOnProcess(Pilot.java:331)

CTAB of current structure:
query.mol
  SciTegic06061413422D

  6  6  0  0  0  0            999 V2000
   -0.7145    0.4125    0.0000 C   0  0
   -0.7145   -0.4125    0.0000 C   0  0
    0.0000   -0.8250    0.0000 C   0  0
    0.7145   -0.4125    0.0000 C   0  0
    0.7145    0.4125    0.0000 C   0  0
    0.0000    0.8250    0.0000 C   0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
M  END
$$$$

---------------------------------

************************************************

Thanks for helping me

Nao

Dear Nao,

First of all deep apologies for answering this late - there was a small problem in our forum notification system (regarding the first post of newly registered users). 

The problem seems to be that you are using an incompatible JChem and Component Collection version combination:

 JChem version : 5.11.3

Component collection version : 2.7.1_j62

This component collection is compatible with JChem versions 6.2.x.

.I suggest to upgrade the JChem library (the content of the lib directory) to a 6.2.x version.

 Or  you may upgrade to the latest 2.8.1 components and JChem 6.3.

Please let us know if you are locked to this JChem version for some specific reason, then I will let you know how to obtain an older version of the component collection.

Best regards,

Szilard

Dear Szilard,

 

Thank you for the reply. That makes sense.

The reason I've installed JChem ver. 5. 11. 3. driver on the pipeline pilot server is that the table I searched was built with JChem ver. 5.11.3.

Do you think the JChem base table should be built with JChem ver. 6. 2. X?

I heard JChem ver. of the driver to search table should be compatible with JChem ver. of the database.

Is that true?

 

Best regards,

Nao

Hi,

That is correct, you should only search / update a JChem table with a compatible software version. (otherwise you will get an error message).

When you connect with a newer version of JChemManager to the database, it will offer you to upgrade all the tables, which in many cases means recalculation of some computed data (e.g. fingerprints) to match the new version. This can take some time depending on the size of the database. After this all software connecting to this JChem table should use this new version.

For more information please see:

http://www.chemaxon.com/jchem/doc/admin/#upgrade

Best regards,

Szilard

Hi Szilard,

 

Thank you for the quick responce.

Everything is in the bag.

 

Best regards,

 

Nao