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berlinguyinca / binbase

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0 values in 132051 for 2 compounds #46

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
2 compounds have 0 values after the netcdf replacement, why?

 Pyruvic acid and lactic acid have several zero replaced values as well as some unknown compounds

Original issue reported on code.google.com by berlinguyinca on 21 Aug 2013 at 9:02

GoogleCodeExporter commented 9 years ago 
mostly related to wrong netcdf files, but one bug:

[06:53:01,831] [INFO ] [id:944364] [replace] [object has no value -> needs to 
be replaced!]
[06:53:01,831] [INFO ] [id:944364] [replace] [current bin: 944364]
[06:53:01,831] [INFO ] [id:944364] [replace] [obtaining retention time for bin: 
0.0 - {id=944364, sample_id=3025043}]
[06:53:01,855] [WARN ] [id:944364] [replace] [no average rt found for this bin! 
falling back]
[06:53:01,855] [INFO ] [id:944364] [replace] [calculating retention time with 
regression for 944364]
[06:53:01,856] [INFO ] [id:944364] [replace] [assuming time: 858144.2623910629]
[06:53:02,018] [ERROR] [id:944364] [replace] [mass: 217]
[06:53:02,018] [ERROR] [id:944364] [replace] [object: 0.0 - {id=944364, 
sample_id=3025043}]
[06:53:02,019] [ERROR] [id:944364] [replace] []
java.lang.NullPointerException
    at java.util.concurrent.ConcurrentHashMap.hash(ConcurrentHashMap.java:333)
    at java.util.concurrent.ConcurrentHashMap.get(ConcurrentHashMap.java:988)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.statistic.replacement.OldReplaceWithQuantIntensity.findMaxIntensity(OldReplaceWithQuantIntensity.java:339)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.statistic.replacement.OldReplaceWithQuantIntensity.replaceAction(OldReplaceWithQuantIntensity.java:147)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.statistic.replacement.OldNetCDFReplacement.obtainNode(OldNetCDFReplacement.java:326)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.statistic.replacement.OldNetCDFReplacement.access$2(OldNetCDFReplacement.java:288)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.statistic.replacement.OldNetCDFReplacement$3.run(OldNetCDFReplacement.java:559)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.statistic.replacement.OldNetCDFReplacement.replaceSingleSample(OldNetCDFReplacement.java:570)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.statistic.replacement.OldNetCDFReplacement.replaceZeros(OldNetCDFReplacement.java:435)
    at edu.ucdavis.genomics.metabolomics.util.statistics.data.SimpleDatafile.replaceRowBased(SimpleDatafile.java:953)
    at edu.ucdavis.genomics.metabolomics.util.statistics.data.SimpleDatafile.replaceZeros(SimpleDatafile.java:966)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.ResultDataFile.replaceZeros(ResultDataFile.java:859)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.StaticStatisticActions.replaceZeros(StaticStatisticActions.java:115)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.StaticStatisticActions.calculateStatistics(StaticStatisticActions.java:1236)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.StaticStatisticActions.transform(StaticStatisticActions.java:1195)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.SimpleStatisticProcessor.localMode(SimpleStatisticProcessor.java:130)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.data.SimpleStatisticProcessor.process(SimpleStatisticProcessor.java:83)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.export.SQLExportService.export(SQLExportService.java:182)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.export.SQLExportService.export(SQLExportService.java:133)
    at edu.ucdavis.genomics.metabolomics.binbase.algorythm.export.SQLExportService$export.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
    at edu.ucdavis.genomics.metabolomics.binbase.dsl.calc.LocalExporter.calculate(LocalExporter.groovy:378)
    at edu.ucdavis.genomics.metabolomics.binbase.dsl.calc.LocalExporter$calculate.callCurrent(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:141)
    at edu.ucdavis.genomics.metabolomics.binbase.dsl.calc.LocalExporter.run(LocalExporter.groovy:79)
    at edu.ucdavis.genomics.metabolomics.binbase.binbase.calculator.GroovyDSLCalculator.main(GroovyDSLCalculator.java:21)

Original comment by berlinguyinca on 30 Aug 2013 at 1:55

GoogleCodeExporter commented 9 years ago 
exception is fixed instead we log a warning, which is related to use not being 
able to find a ion trace for this particular ion

Original comment by berlinguyinca on 30 Aug 2013 at 3:06

GoogleCodeExporter commented 9 years ago 
new algorithm automatically adjusts the search range by factor 2, to hope to 
find some ions.

Original comment by berlinguyinca on 30 Aug 2013 at 3:37