Abacus fail

Yesterday Emma was concerned about Rhonda’s Abacus file. If fact there were differences. I created a new Abacus parameter file

# ABACUS parameter file
# Generated on: 2017Feb14_1919

# Name to give the database

# Name of protXML file corresponding to merged/combined results

# The directory that contains the pepXML and protXML files

# The name of the file where results will be saved to

# The minimum PeptideProphet score the best peptide match of a protein must have

# The minimum PeptideProphet score a peptide must have in order to be even considered by Abacus

# E.P.I: Experimental Peptide-probability Inclusion threshold
# If a protein does not contain at least one peptide exceeding this PeptideProphet score, none of the
# peptide evidence for this protein will be considered. This is applied on an experiment by experiment case.

# The minimum ProteinProphet score a protein group must have in the COMBINED file

# The path the the FASTA formatted file used for the original protein search
# Relative paths are allowed

# If true, Abacus will write ALL protein IDs belonging to a group in the COMBINED file
# Protein IDs starting with ':::' are additional identifiers from the same protein group in
# the COMBINED file. The representative protein for the group does not start with ':::'

# The keep the HyperSQL database files that are created after the program is done

# Should the peptide weights be recalculated in the individual experiment XML files.
# Useful for peptides that are highly degenerate within a single protein groups

# Spectral count data will be reported in NSAF format.
# NSAF = _N_ormalized _S_pectral _A_bundance _F_actor
# For a detailed explanation of this method refer to this pubmed link:
# http://www.ncbi.nlm.nih.gov/pubmed/20166708
# Abacus reports NSAF values multiplied by a scaling factor. This is done to
# control for numeric underflow (ie: really small numbers). The scaling factor
# that is used is called the NSAF_FACTOR and is reported during runtime in
# case you would like to rescale your data.

# If you are using decoy proteins in your searches, specify the first few
# characters of the label indicating decoy proteins here

# Output format that will be produced by this parameter file

In then proceed to create a new working directory and move all the files created as doing this

I proceed to add the new Abacus file (and remove the old one) and ran

java -Xmx16g -jar /home/shared/abacus/abacus.jar -p \

Here is stdout

of concern:

 Adding data from X20161205_SAMPLE_8A

Creating NSAF values table (protein-centric)
  NSAF_FACTOR = 10^5 = 100000.0
java.sql.SQLSyntaxErrorException: user lacks privilege or object not found: NAN
	at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
	at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
	at org.hsqldb.jdbc.JDBCStatement.fetchResult(Unknown Source)
	at org.hsqldb.jdbc.JDBCStatement.executeUpdate(Unknown Source)
	at abacus.hyperSQLObject.getNSAF_values_prot(hyperSQLObject.java:2961)
	at abacus.abacus.main(abacus.java:221)
	at mainFunction.mainFunction.main(mainFunction.java:49)
Caused by: org.hsqldb.HsqlException: user lacks privilege or object not found: NAN
	at org.hsqldb.error.Error.error(Unknown Source)
	at org.hsqldb.error.Error.error(Unknown Source)
	at org.hsqldb.ExpressionColumn.checkColumnsResolved(Unknown Source)
	at org.hsqldb.ParserDML.resolveUpdateExpressions(Unknown Source)
	at org.hsqldb.ParserDML.compileUpdateStatement(Unknown Source)
	at org.hsqldb.ParserCommand.compilePart(Unknown Source)
	at org.hsqldb.ParserCommand.compileStatements(Unknown Source)
	at org.hsqldb.Session.executeDirectStatement(Unknown Source)
	at org.hsqldb.Session.execute(Unknown Source)
	... 5 more

And no output from Abacus.

Written on February 15, 2017