Data File size limit is reached

[Simon]

Hi everyone,

When I run abacus with data of 200 pull down experiments I reach 90%
completion, followed by an error message "Data File size limit is
reached" (full message see below). The samples are of moderate
complexity with around 100 proteins with protein prophet probability
>0.9. Is my data set simply to big or is there another way abacus can
handle this?

I use all standard parameters and the NSAF option is on. The file size
of the generated database file is 17.2GB

Thanks,
Simon


Here the full terminal output:

2012-01-04T15:35:20.011+0100 SEVERE data file reached maximum size
ABACUSDB.data
2012-01-04T15:35:20.083+0100 SEVERE null
java.sql.SQLException: Data File size limit is reached
at org.hsqldb.jdbc.Util.sqlException(Util.java:418)
at org.hsqldb.jdbc.Util.sqlException(Util.java:247)
at org.hsqldb.jdbc.JDBCStatement.fetchResult(JDBCStatement.java:1830)
at org.hsqldb.jdbc.JDBCStatement.executeUpdate(JDBCStatement.java:
207)
at abacus.hyperSQLObject.reformat_results(hyperSQLObject.java:2959)
at abacus.hyperSQLObject.getNSAF_values_prot(hyperSQLObject.java:
2848)
at abacus.abacusUI.workThread.run(abacusUI.java:2633)
Caused by: org.hsqldb.HsqlException: Data File size limit is reached
at org.hsqldb.error.Error.error(Error.java:134)
at org.hsqldb.error.Error.error(Error.java:104)
at org.hsqldb.persist.DataFileCache.setFilePos(DataFileCache.java:
703)
at org.hsqldb.persist.DataFileCache.add(DataFileCache.java:729)
at org.hsqldb.persist.RowStoreAVLDisk.add(RowStoreAVLDisk.java:132)
at
org.hsqldb.persist.RowStoreAVLDisk.getNewCachedObject(RowStoreAVLDisk.java:
153)
at org.hsqldb.Table.insertSingleRow(Table.java:2551)
at org.hsqldb.StatementDML.update(StatementDML.java:1032)
at org.hsqldb.StatementDML.executeUpdateStatement(StatementDML.java:
541)
at org.hsqldb.StatementDML.getResult(StatementDML.java:196)
at org.hsqldb.StatementDMQL.execute(StatementDMQL.java:190)
at org.hsqldb.Session.executeCompiledStatement(Session.java:1344)
at org.hsqldb.Session.executeDirectStatement(Session.java:1227)
at org.hsqldb.Session.execute(Session.java:1013)
at org.hsqldb.jdbc.JDBCStatement.fetchResult(JDBCStatement.java:1822)

[GATTACA]

Hi Simon,

Here are a few questions I have and easy things to try out:

1) Are you including a combined pep.xml file for abacus?
What I mean is: do you have an interact-combined.prot.xml file and a
interact-combined.pep.xml file?
If so, delete the interact-combined.pep.xml file. Abacus does not use
this at all but will read it in if its found in the same folder as the
pep.xml files.

2) How much physical memory do you have on your computer? Is a 64bit
operating system?
If you are running a 64-bit OS try executing this command from the
terminal/command prompt:
java -d64 -jar abacus.jar
This will force Java to run in 64-bit mode and use > 4GB of available
memory if needed.

Some users have complained that Abacus crashes on them in Windows if
it is not called from the command prompt as opposed to double clicking
on the icon. I don't have a Windows computer to test this on but users
have told me that the java -d64 abacus.jar option seems to work for
them.

3) If you run Abacus without NSAF does it run to completion?


If none of the above work, could you email me the abacus input file
for the parameters that you are using?

Hope some of this helps.
Damian

[Simon]

Hi Damian,

Thank you for the quick reply. You are right, the combined-
interact.pep.xml did cause the problem. Now it works like a charm
incl. NSAF and everything.

Thanks a lot ,
Simon

[Damian]

Glad to hear it.
Let me know if you have any further issues.

Damian

---------------------------------------------------------------
Fermin and Choudhuri Enterprises Inc.
Damian Fermin, Ph.D.
damian...@gmail.com
http://damianfermin.com
734-395-7664