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Loading GO annotations - java error

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Loading GO annotations - java error rob_ewing50  2008-09-02 12:19
Status: Closed
 
When I try and load the GO annotations I get this:

Loading GO annotations failed with the following exception:

java.lang.ArrayIndexOutOfBoundsException: 4
       at org.labkey.ms2.protein.tools.GoLoader.loadSingleGoFile(GoLoader.java:213)
       at org.labkey.ms2.protein.tools.GoLoader.loadGoFromGz(GoLoader.java:141)
       at org.labkey.ms2.protein.tools.GoLoader.access$200(GoLoader.java:32)
       at org.labkey.ms2.protein.tools.GoLoader$1.run(GoLoader.java:101)
       at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
       at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
       at java.util.concurrent.FutureTask.run(FutureTask.java:123)
       at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
       at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)



See below for complete log

Searching for the latest GO annotation files at ftp.geneontology.org
Starting to download go_200808-termdb-tables.tar.gz from ftp.geneontology.org
Finished downloading go_200808-termdb-tables.tar.gz

Starting to load GO annotation files

Clearing table prot.gotermdefinition
Starting to load term_definition.txt
5000 rows loaded
10000 rows loaded
15000 rows loaded
20000 rows loaded
25000 rows loaded
Completed loading term_definition.txt

Clearing table prot.goterm2term
Starting to load term2term.txt
5000 rows loaded
10000 rows loaded
15000 rows loaded
20000 rows loaded
25000 rows loaded
30000 rows loaded
35000 rows loaded
40000 rows loaded
Completed loading term2term.txt

Clearing table prot.gotermsynonym
Starting to load term_synonym.txt
Loading GO annotations failed with the following exception:

java.lang.ArrayIndexOutOfBoundsException: 4
       at org.labkey.ms2.protein.tools.GoLoader.loadSingleGoFile(GoLoader.java:213)
       at org.labkey.ms2.protein.tools.GoLoader.loadGoFromGz(GoLoader.java:141)
       at org.labkey.ms2.protein.tools.GoLoader.access$200(GoLoader.java:32)
       at org.labkey.ms2.protein.tools.GoLoader$1.run(GoLoader.java:101)
       at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
       at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
       at java.util.concurrent.FutureTask.run(FutureTask.java:123)
       at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
       at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
       at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
       at java.lang.Thread.run(Thread.java:595)

       at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
       at java.lang.Thread.run(Thread.java:595)
 
 
rob_ewing50 responded:  2008-09-03 08:02
It seems as though there is an issue with later GO releases. If I run the process manually, and download the files from an earlier GO version (March 2008) I do not have the same issue. I have tried with several releases of GO - anything later than about May 2008 does not work and gives the error as above.
 
adam responded:  2008-09-03 14:11
Thanks for the report. The GO file format changed in May. This was noticed in June (https://www.labkey.org/announcements/home/Developer/Forum/thread.view?rowId=2531) and fixed shortly after in release 8.2 (https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=6085). I've confirmed that 8.2 and our upcoming 8.3 release load the latest file (go_200808-termdb-tables.tar.gz) just fine.

I'm assuming you're running 8.1 or earlier; please post ASAP if you're using 8.2 or later. I suggest upgrading to 8.2 or using manual upload with one of the earlier files if you can't upgrade for some reason.

Adam