[InterMine Dev] Need InterMine help: org.intermine.objectstore.ObjectStoreException: Error in worker thread

Shamimuzzaman, Md shamimuzzamanm at missouri.edu
Mon Jun 17 16:32:32 BST 2019


Thanks Julie.

We will run with the flag and let you know the error message.


Shamim

________________________________
From: Julie Sullivan <julie at intermine.org>
Sent: Monday, June 17, 2019 10:22:22 AM
To: Shamimuzzaman, Md; InterMine Devs
Subject: Fwd: Need InterMine help: org.intermine.objectstore.ObjectStoreException: Error in worker thread

Hi Shamim!

Can you run that command again with the "--stacktrace" flag?

The error message says "error in worker thread" but doesn't say what
caused the error.

I am hoping "--stacktrace" gives us a better error message! :)

Thanks!
Julie


-------- Forwarded Message --------
Subject:         Need InterMine help:
org.intermine.objectstore.ObjectStoreException: Error in worker thread
Date:    Mon, 17 Jun 2019 15:19:48 +0000
From:    Shamimuzzaman, Md <shamimuzzamanm at missouri.edu>




Hi,

This is Shamim from University of Missouri. I am working with professor
Christine Elsik.
We are having an issue while loading dbsnp dataset. We loaded several of
our dbsnp datasets successfully.
Suddenly we started to get the following error message
Error processing data: org.intermine.objectstore.ObjectStoreException:
Error in worker thread

I copied and pasted entire message below

[integrate] CSQ: [T, intergenic_variant]
[integrate] RSID: rs1111455060
[integrate] CSQ: [C, intergenic_variant]
       [null] Exiting
/db/FAANGMine_release_1.1_april2019/elsiklab-intermine/bio/sources/dbsnp-variation/build.xml.

BUILD FAILED
/db/FAANGMine_release_1.1_april2019/elsiklab-intermine/imbuild/integrate.xml:54:
The following error occurred while executing this line:
/db/FAANGMine_release_1.1_april2019/elsiklab-intermine/bio/sources/dbsnp-variation/build.xml:23:
Error processing data: org.intermine.objectstore.ObjectStoreException:
Error in worker thread
          at
org.intermine.bio.dataconversion.DbsnpVariationDirectDataLoaderTask.processFile(DbsnpVariationDirectDataLoaderTask.java:168)
          at
org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:50)
          at
org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:170)
          at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
          at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
          at java.lang.reflect.Method.invoke(Method.java:498)
          at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
          at org.apache.tools.ant.Task.perform(Task.java:350)
          at org.apache.tools.ant.Target.execute(Target.java:448)
          at org.apache.tools.ant.Target.performTasks(Target.java:469)
          at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
          at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:36)
          at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
          at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:446)
          at org.intermine.task.Integrate.performAction(Integrate.java:219)
          at org.intermine.task.Integrate.performAction(Integrate.java:132)
          at org.intermine.task.Integrate.execute(Integrate.java:123)
          at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
          at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
          at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
          at java.lang.reflect.Method.invoke(Method.java:498)
          at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
          at org.apache.tools.ant.Task.perform(Task.java:350)
          at org.apache.tools.ant.Target.execute(Target.java:448)
          at org.apache.tools.ant.Target.performTasks(Target.java:469)
          at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
          at org.apache.tools.ant.Project.executeTarget(Project.java:1370)
          at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
          at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
          at org.apache.tools.ant.Main.runBuild(Main.java:849)
          at org.apache.tools.ant.Main.startAnt(Main.java:228)
          at org.apache.tools.ant.launch.Launcher.run(Launcher.java:283)
          at org.apache.tools.ant.launch.Launcher.main(Launcher.java:101)

Total time: 36 minutes 23 seconds
[Thread-6] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
db.production is shutting down.


Thanks
Shamim

Md Shamimuzzaman, PhD
Research Scientist
Animal Sciences Research Center
University of Missouri at Columbia
Email: shamimuzzamanm at missouri.edu

Cell: 217-721-2545

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