Error running abacus

Lotta Happonen

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Jun 15, 2015, 8:31:36 AM6/15/15

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Dear all,

I get the following error when running abacus on my files:

Appending additional protein identifiers to final output

java.sql.SQLException: statement is not in batch mode

at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)

at org.hsqldb.jdbc.JDBCUtil.sqlExceptionSQL(Unknown Source)

at org.hsqldb.jdbc.JDBCPreparedStatement.executeBatch(Unknown Source)

at abacus.hyperSQLObject.addProteinLengths(hyperSQLObject.java:2008)

at abacus.abacus.main(abacus.java:226)

at mainFunction.mainFunction.main(mainFunction.java:44)

Caused by: org.hsqldb.HsqlException: statement is not in batch mode

at org.hsqldb.error.Error.error(Unknown Source)

... 5 more

I have my individual interact*pep.xml, interact*prot.xml as well as interact-combined.prot.xml files, and the fasta-file in the folder in which I'm trying to run abacus (in addition to the abacus parameters file). We've tested this on other files on the same server, and in these cases abacus works fine. I have regenerated (a new) fasta-file with decoys several times, as well as searched the data. Everything has been double checked for typos.

Any other suggestions? Or could there be a problem with the original ms-files?

Best,

Lotta

Damian

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Jun 15, 2015, 9:51:24 AM6/15/15

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Hi Lotta

The error message you are getting appears to be related to the fasta file.
Can you try running Abacus without specifying the FASTA file?
I'm not sure what version you are running but the latest one should allow you to leave the fasta file field blank.

Damian

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Lotta Happonen

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Jun 16, 2015, 5:33:07 AM6/16/15

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Hi Damian,

thanks!

I reanalyzed the data using another fasta-file, and now everything (abacus) worked fine.