# # ABACUS parameter file # Generated on: 2017Feb14_1919 # # Name to give the database dbName=Cg_Giga_cont_AA.fa # Name of protXML file corresponding to merged/combined results combinedFile=/home/steven/bioinfo/021417/interact-COMBINED.prot.xml # The directory that contains the pepXML and protXML files srcDir=/home/steven/bioinfo/021417 # The name of the file where results will be saved to outputFile=/home/steven/bioinfo/021417/ABACUS_output.tsv # The minimum PeptideProphet score the best peptide match of a protein must have maxIniProbTH=0.99 # The minimum PeptideProphet score a peptide must have in order to be even considered by Abacus iniProbTH=0.50 # 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. epiTH=0 # The minimum ProteinProphet score a protein group must have in the COMBINED file minCombinedFilePw=0.90 # The path the the FASTA formatted file used for the original protein search # Relative paths are allowed fasta=Cg_Giga_cont_AA.fa # 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 ':::' verboseResults=false # The keep the HyperSQL database files that are created after the program is done keepDB=false # Should the peptide weights be recalculated in the individual experiment XML files. # Useful for peptides that are highly degenerate within a single protein groups recalcPepWts=false # 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. asNSAF=true # If you are using decoy proteins in your searches, specify the first few # characters of the label indicating decoy proteins here decoyTag=DECOY_ # Output format that will be produced by this parameter file output=Default
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 \ Abacus-01.param
Here is stdout
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