Fwd: Need InterMine help: org.intermine.objectstore.ObjectStoreException: Error in worker thread

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Fwd: Need InterMine help: org.intermine.objectstore.ObjectStoreException: Error in worker thread

Julie Sullivan-2
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 <[hidden email]>




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: [hidden email]

Cell: 217-721-2545

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Re: Need InterMine help: org.intermine.objectstore.ObjectStoreException: Error in worker thread

Shamimuzzaman, Md

Thanks Julie.

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


Shamim


From: Julie Sullivan <[hidden email]>
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 <[hidden email]>




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: [hidden email]

Cell: 217-721-2545


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev