Error related to gap filler and empty document

[Nathaly Reyes Garcés]

Hi 

This is my first time using IDEOM, and I'm getting some errors. I created folders with my samples, each folder has mzXML data and .peakml. Now, I can see that there were created four more folders (chromatograms(which is empty), combined, combined_RSD_filter, combined_RSD_rejected,). In addition, at in the same folder where I see all the folders, there are four files (combined.peakml,  combined_noisef.peakml, combined_highintensity.peakml,combined_sfdet.peakml) which are 0 bytes plus a file called "error" saying the following:

java.io.FileNotFoundException: highintensity_gapfilled.peakml (The system cannot find the file specified)

at java.io.FileInputStream.open(Native Method)

at java.io.FileInputStream.<init>(Unknown Source)

at java.io.FileInputStream.<init>(Unknown Source)

at mzmatch.ipeak.sort.RelatedPeaks.main(RelatedPeaks.java:257) 

Below I'm pasting what I got in the R window. I appreciate any help on this.

Nathaly

Loading 'combined.peakml'.

domsax.XmlParserException: Premature end of file.

        at domsax.XmlParser.parse(XmlParser.java:115)

        at peakml.io.peakml.PeakMLParser.run(PeakMLParser.java:402)

        at peakml.io.peakml.PeakMLParser.parse(PeakMLParser.java:174)

        at peakml.io.peakml.PeakMLParser.parse(PeakMLParser.java:108)

        at mzmatch.ipeak.filter.NoiseFilter.main(NoiseFilter.java:252)

Java HotSpot(TM) Client VM warning: MaxNewSize (1048576k) is equal to or greater than the entire heap (1024000k).  A new max generation size of 1023744k will be used.

> mzmatch.ipeak.filter.SimpleFilter(i="combined_noisef.peakml", o="combined_sfdet.peakml", mindetections=3, JHeapSize=1000)

domsax.XmlParserException: Premature end of file.

        at domsax.XmlParser.parse(XmlParser.java:115)

        at peakml.io.peakml.PeakMLParser.run(PeakMLParser.java:402)

        at peakml.io.peakml.PeakMLParser.parse(PeakMLParser.java:174)

        at peakml.io.peakml.PeakMLParser.parse(PeakMLParser.java:108)

        at mzmatch.ipeak.filter.SimpleFilter.main(SimpleFilter.java:306)

Java HotSpot(TM) Client VM warning: MaxNewSize (1048576k) is equal to or greater than the entire heap (1024000k).  A new max generation size of 1023744k will be used.

> mzmatch.ipeak.filter.SimpleFilter(i="combined_sfdet.peakml", o="combined_highintensity.peakml", minintensity=3000, JHeapSize=1000)

domsax.XmlParserException: Premature end of file.

        at domsax.XmlParser.parse(XmlParser.java:115)

        at peakml.io.peakml.PeakMLParser.run(PeakMLParser.java:402)

        at peakml.io.peakml.PeakMLParser.parse(PeakMLParser.java:174)

        at peakml.io.peakml.PeakMLParser.parse(PeakMLParser.java:108)

        at mzmatch.ipeak.filter.SimpleFilter.main(SimpleFilter.java:306)

Java HotSpot(TM) Client VM warning: MaxNewSize (1048576k) is equal to or greater than the entire heap (1024000k).  A new max generation size of 1023744k will be used.

> PeakML.GapFiller(filename = "combined_highintensity.peakml", ionisation = "detect", Rawpath = NULL, outputfile = "highintensity_gapfilled.peakml", ppm=5, rtwin = 0)

Document is empty

Start tag expected, '<' not found

Error: 1: Document is empty

2: Start tag expected, '<' not found

Timing stopped at: 0 0 0.14 

Timing stopped at: 0.05 0 0.19 

> mzmatch.ipeak.sort.RelatedPeaks (i="highintensity_gapfilled.peakml",v=T,o="mzMatch_output.peakml",basepeaks="mzMatch_basepeaks.peakml",ppm=3,rtwindow=6, JHeapSize=1000)

 ------------------------------------------------------

| Copyright 2007-2009

| Groningen Bioinformatics Centre

| University of Groningen

|

| RelatedPeaks 1.0.0

|

| libraries:

|  - jfreechart    1.0.13

|  - itext         2.1.7

|  - jama          1.0.2

|  - lma           1.4.0

|  - cmdline       2.0.0

|  - domsax        1.1.0

|  - peakml        1.0.0

|  - mzmatch       1.0.2

 ------------------------------------------------------

Options {

  minrt:     -1.0

  rtwindow:  6.0

  v:         true

  basepeaks: mzMatch_basepeaks.peakml

  h:         false

  i:         highintensity_gapfilled.peakml

  ppm:       3.0

  o:         mzMatch_output.peakml

}

loading data

java.io.FileNotFoundException: highintensity_gapfilled.peakml (The system cannot find the file specified)

        at java.io.FileInputStream.open(Native Method)

        at java.io.FileInputStream.<init>(Unknown Source)

        at java.io.FileInputStream.<init>(Unknown Source)

        at mzmatch.ipeak.sort.RelatedPeaks.main(RelatedPeaks.java:257)

Java HotSpot(TM) Client VM warning: MaxNewSize (1048576k) is equal to or greater than the entire heap (1024000k).  A new max generation size of 1023744k will be used.

> annot <- paste("relation.id,relation.ship,codadw,charge")

> mzmatch.ipeak.convert.ConvertToText (i="mzMatch_output.peakml",o="mzMATCHoutput.txt",v=T,annotations=annot, JHeapSize=1000)

 ------------------------------------------------------

| Copyright 2007-2009

| Groningen Bioinformatics Centre

| University of Groningen

|

| ConvertToText 1.0.1

|

| libraries:

|  - jfreechart    1.0.13

|  - itext         2.1.7

|  - jama          1.0.2

|  - lma           1.4.0

|  - cmdline       2.0.0

|  - domsax        1.1.0

|  - peakml        1.0.0

|  - mzmatch       1.0.2

 ------------------------------------------------------

Options {

  databases:   []

  v:           true

  h:           false

  i:           [mzMatch_output.peakml]

  annotations: [relation.id, relation.ship, codadw, charge]

  o:           mzMATCHoutput.txt

}

[ERROR]: the input-file 'mzMatch_output.peakml' does not exist.

Java HotSpot(TM) Client VM warning: MaxNewSize (1048576k) is equal to or greater than the entire heap (1024000k).  A new max generation size of 1023744k will be used.

> 

> # Processing finished!     Now extracting chromatogram images for each peak.

> chromdir <- "chromatograms"

> dir.create(chromdir)

Warning message:

In dir.create(chromdir) : 'chromatograms' already exists

> PeakMLData <- PeakML.Read("mzMatch_output.peakml",Rawpath=NULL)

Error: XML content does not seem to be XML: 'mzMatch_output.peakml'

Timing stopped at: 0 0 0 

> peakIDlist <- c(1:length(unique(PeakMLData$peakDataMtx[,10])))

Error in unique(PeakMLData$peakDataMtx[, 10]) : 

  error in evaluating the argument 'x' in selecting a method for function 'unique': Error: object 'PeakMLData' not found

> sampnames <- PeakMLData$sampleNames

Error: object 'PeakMLData' not found

> sampleslist<-c(1:max(PeakMLData$peakDataMtx[,9]))

Error: object 'PeakMLData' not found

> groupsets <- max(PeakMLData$peakDataMtx[,11])

Error: object 'PeakMLData' not found

> if (groupsets!=1) {samplegroups <- PeakMLData$phenoData} else {samplegroups <- sampnames}

Error: object 'groupsets' not found

> classnumbers <- samplegroups

Error: object 'samplegroups' not found

> for (i in 1:length(unique(samplegroups))){classnumbers <- sub(unique(classnumbers)[i], i, classnumbers)}

Error in unique(samplegroups) : 

  error in evaluating the argument 'x' in selecting a method for function 'unique': Error: object 'samplegroups' not found

> for (a in 1:length(peakIDlist)){peakID <- peakIDlist[a]

+ hits <- which(PeakMLData$peakDataMtx[,10]==peakID)

+ intslist <- vector ("list")

+ rtlist <- vector ("list")

+ for (i in 1:length(hits)){intslist[[i]] <- PeakMLData$chromDataList[[hits[i]]][2,]

+ rtlist[[i]] <- (PeakMLData$chromDataList[[hits[i]]][3,]) / 60 }

+ maxint <- max(unlist(intslist))

+ minrt <-  min (unlist(rtlist))

+ maxrt <- max (unlist(rtlist))

+ samplenumbers <- PeakMLData$peakDataMtx[hits,9]

+ myfilename <- paste(getwd(),"/",chromdir,"/",peakID,".png",sep="")

+ png(myfilename, width = 350, height = 300)

+ lw = 0.2

+ par(fig=c(0,1-lw,0,1))

+ plot (1,1,xlab="RT (m)", ylab="Intensity", pch="", xlim=c(minrt,maxrt), ylim=c(0,maxint))

+ for (i in 1:length(hits)){if (PeakMLData$peakDataMtx[hits[i],9] %in% sampleslist==TRUE){

+ points (rtlist[[i]], intslist[[i]], type="l", col=classnumbers[samplenumbers [i]])}}

+ par(fig=c(0,1,0,1))

+ lpos <- par("usr")[2]-(lw /(1-lw ))*(par("usr")[2]-par("usr")[1])

+ legend (lpos, par("usr")[4], text.col=unique(classnumbers[sampleslist]), unique(samplegroups[sampleslist]), cex=0.8,xpd=TRUE)

+ dev.off()}

Error: object 'peakIDlist' not found

> 

[Darren Creek]

Hi Nathaly,
The error is occurring earlier in the pipeline and therefore sequential files are not being created for the following steps.  In your case the first error occurs before the section of text provided in your email. Please scroll up and find where the first error occurs.
It is often an issue with your version of Java or the RAM allocation being incompatible with your machine. Consider updating/modifying these depending on the nature of the first error.
Cheers,
Darren

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