run error

[Jimmy]

Damian

I'm getting this error when running Abacus on a run with 42 input files.  In the console, it gets to "Creating ProtXML table" and then the following gets dumped and the process seems to just die.  Let me know if you have any ideas on what to try/change.  Thanks.

ls Sep 04, 2015 9:22:44 AM abacus.abacusUI.workThread run

SEVERE: null

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

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

        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.makeProtXMLTable(hyperSQLObject.java:575)

        at abacus.abacusUI.workThread.run(abacusUI.java:2814)

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

back

ls: cannot access back: No such file or directory

[Damian]

Hi Jimmy

I've seen this error before and the cause varies from case to case.
The problem has to do with the batch insertion of data into the temporary database.
Originally what protein database did you use? I ask because if the protein names are really long they may exceed the size allocated for the protid field.

You might be able to work around it by saving the  menu options to a parameter file and then running abacus from the terminal without the GUI. I don't know why this works but some users have told me they get pass the error doing it this way.

Damian

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[Jimmy]

The database is some marine metagenome sequence database.  Regarding the protein name length, is the issue with the length of the full protein description line or the first "word" or accession in the description line?  I'll try running it w/o the GUI first and then see about manipulating the database if that doesn't work.

[Damian]

I have hard coded for detection of Uniprot/Swissprot and RefSeq fasta header lines.
Anything else and abacus takes up the first space character that is encountered. If the protein ID is trimmed at the first space character and the resulting protein ID is still > 100 characters you get problems down the line.

Let me know if you still have issues after running without the GUI.

Damian

On 09/04/2015 01:41 PM, Jimmy wrote:

The database is some marine metagenome sequence database.  Regarding the protein name length, is the issue with the length of the full protein description line or the first "word" or accession in the description line?  I'll try running it w/o the GUI first and then see about manipulating the database if that doesn't work.

[Jimmy]

Damian,

I started an Abacus command line run over the long weekend and see that the run failed.  In the slim case that the error output could be helpful in determining what went wrong, I pasted the output below.  fwiw, I do know that the protein IDs (to the first space character in the description line) have a maximum of 28 characters so the ID length isn't an issue.

***********************************

        Abacus

        Version: 2.5

***********************************

Developed and written by: Damian Fermin and Alexey Nesvizhskii

Copyright 2010 Damian Fermin

Licensed under the Apache License, Version 2.0 (the "License");

you may not use this file except in compliance with the License.

You may obtain a copy of the License at 

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software

distributed under the License is distributed on an "AS IS" BASIS,

WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and

limitations under the License.

Parameters for this execution:

        Source directory: '/data/abacus'

        DB name:          'ABACUSDB'

        Output file:      '/data/abacus/ABACUS_output.tsv'

        Combined file P:   0.9

        iniProb threshold: 0.5

        maxIniProb:        0.99

        Keep DB files:     false

        Recalc Pep Wts:    false

        Output format:     Default

No fasta file was given so protein lengths will not be reported

Loading protXML files

Parsing protXML [ 1 of 1 ]:  interact-COMBINED.prot.xml

   :

   :

   :

Creating srcFileTags table

Creating combined table from 'interact-COMBINED.prot.xml'

  Curating interact-COMBINED.prot.xml

  Recalculating peptide weights for combined

Creating protXML table

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

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

        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.makeProtXMLTable(hyperSQLObject.java:575)

        at abacus.abacus.main(abacus.java:192)

        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)

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

        ... 5 more

[Damian]

This is weird. Is there some way I could take a look at these files and try a few things with them and Abacus?

Damian

[Jimmy]

Yes, I'll send you a link to download the files offline once I gather a smaller set and can confirm the error appears there too.

[Damian]

Hey Jimmy I just noticed that you are missing some files.
For Abacus you need K pepXML files and K+1 protXML files.

For this particular data set you  should have 3 protXML files:
interact-2014_Sept_08_BeringSea50.prot.xml
interact-2014_Sept_08_BeringSea51.prot.xml
interact-COMBINED.prot.xml

And 2 pepXML files:
interact-2014_Sept_08_BeringSea50.pep.xml
interact-2014_Sept_08_BeringSea51.pep.xml

I overlooked your snippet of screen output where it stated Parsing protXML [ 1 of 1 ] (just assumed more protXML file names followed and you weren't showing them)

Try providing Abacus the missing protXML files, this should clear up your problem.
Damian

[Jimmy]

Thanks for debugging this Damian; I knew it had to be some stupid self-inflicted error like this.