Abacus Freezing at 30%

[Wallace Chan]

When I run Abacus, I get to 'Creating protXML table' before it freezes. The error I get from the command prompt is as follows:

SEVERE: null
java.sql.SQLException: statement is not in batch mode
    at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
    at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
    at org.hsqldb.jdbc.Util.sqlExceptionSQL(Unknown Source)
    at org.hsqldb.jdbc.JDBCPreparedStatement.executeBatch(Unknown Source)
    at abacus.hyperSQLObject.makeProtXMLTable(hyperSQLObject.java:532)
    at abacus.abacusUI.workThread.run(abacusUI.java:2862)
Caused by: org.hsqldb.HsqlException: statement is not in batch mode
    at org.hsqldb.error.Error.error(Unknown Source)
    at org.hsqldb.error.Error.error(Unknown Source)
    ... 4 more

I saw another post that said clearing the options would help, but it didn't. Another post also stated to run in the command prompt, which I am doing. Any help would be greatly appreciated!


Wallace

[Damian]

Hi Wallace,

Can you send me a the names of all the files you are trying to run through Abacus?

Thanks,
Damian

Wallace Chan wrote:

--
You received this message because you are subscribed to the Google
Groups "Abacus Support" group.
To unsubscribe from this group and stop receiving emails from it, send
an email to abacus-suppor...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

[kswea...@systemsbiology.org]

Was there any resolution to this problem? I am attempting to run Abacus on iProphet results from two different search engines combined, and I got the exact same error.

[kswea...@systemsbiology.org]

I believe I have found the solution, so I wanted to post it here. I have been able to reproduce the problem of the program freezing at 30% when there is not an interact.prot.xml file for each input interact.pep.xml. Likewise, I can reproduce the problem of the program freezing at 70% if the individual interact.pep.xml files are not present.

I commonly search my data separately with XTandem and Comet. I run PeptideProphet separately on each batch of files. I then combine my comet.interact.pep.xml file with my tandem.interact.pep.xml file into a single interact.iproph.pep.xml file, and then run ProteinProphet on that file. In order to run Abacus, I needed to run ProteinProphet and produce a comet.interact.prot.xml and a tandem.interact.prot.xml file.

I had to read the paper and the tutorial a couple of times to fully grasp this. In summary, here is how you need to set up your data in order to run Abacus.

Any number of <filename>.pep.xml search engine output files are input into the TPP (InteractParser-->RefreshParser-->PeptideProphetParser) and produce a single Experiment.interact.pep.xml file.

Each Experiment.interact.pep.xml must be run through ProteinProphet to produce a Experiment.interact.prot.xml file. 

If there are multiple Experiment.interact.pep.xml files (for example, combining different search engines in iProphet or combining different biological replicates), then you must run Experiment-1.interact.pep.xml, Experiment-2.interact.pep.xml...Experiment-n.interact.pep.xml through ProteinProphet together and generate a combined COMBINED.interact.prot.xml.

All of the interact.pep.xml and interact.prot.xml files must be in the directory where Abacus is run.