help with error please
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Brad Evans
Mar 10, 2014, 11:53:35 AM3/10/14
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I am attempting to test IDEOM and I keep getting multiple error. Here is the output in the R GUI:
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
During startup - Warning message:
class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
> setwd("U:/Research/Jaya/IDEOM_Test_Lite")
>
> library (rJava)
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)
Loading required package: xcms
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:rJava’:
anyDuplicated, duplicated, sort, unique
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘xcms’
The following objects are masked from ‘package:Biobase’:
phenoData, phenoData<-
Loading required package: XML
Loading required package: snow
Attaching package: ‘snow’
The following objects are masked from ‘package:BiocGenerics’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parApply, parCapply, parLapply, parRapply, parSapply
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster
Loading required package: caTools
Loading required package: bitops
Loading required package: tcltk
Loading required package: ptw
Loading required package: gplots
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
> mzmatch.init (6000)
C:/Users/BEvans/Documents/R/win-library/3.0/mzmatch.R/java/mzmatch.jar
>
> rawfiles <- dir (full.names=TRUE,pattern="\\.mzXML*",recursive=TRUE)
> outputfiles <- paste(sub(".mzXML*","",rawfiles),".peakml",sep="")
> for (i in 1:length(rawfiles)){xset <- xcmsSet(rawfiles[i], method='centWave', ppm=10, peakwidth=c(15,100), snthresh=10, prefilter=c(3,1000), integrate=1, mzdiff=0.001, verbose.columns=TRUE, fitgauss=FALSE, nSlaves=1)
+ PeakML.xcms.write.SingleMeasurement (xset=xset,filename=outputfiles[i],ionisation="positive",addscans=2,writeRejected=FALSE,ApodisationFilter=TRUE)}
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
missing values in 'row.names' are not allowed
>
> MainClasses <- dir ()
> dir.create ("combined_RSD_filtered")
> dir.create ("combined_RSD_rejected")
> dir.create ("combined")
> for (i in 1:length(MainClasses)){FILESf <- dir (MainClasses[i],full.names=TRUE,pattern="\\.peakml$",recursive=TRUE)
+ OUTPUTf <- paste ("combined/",MainClasses[i],".peakml",sep="")
+ if(length(FILESf)>0){mzmatch.ipeak.Combine (i=paste(FILESf,collapse=","),v=T,rtwindow=30,o=OUTPUTf,combination="set",ppm=5,label=paste(MainClasses[i],sep=""), JHeapSize=6000)
+ RSDf <- paste ("combined_RSD_filtered/",MainClasses[i],".peakml",sep="")
+ REJf <- paste ("combined_RSD_rejected/",MainClasses[i],".peakml",sep="")
+ if(length(FILESf)>1) mzmatch.ipeak.filter.RSDFilter(i=OUTPUTf,o=RSDf,rejected=REJf,rsd=0.8, JHeapSize=6000) else file.copy(OUTPUTf,RSDf)}}
> INPUTDIR <- "combined_RSD_filtered"
> FILESf <- dir (INPUTDIR,full.names=TRUE,pattern="\\.peakml$")
> mzmatch.ipeak.Combine(i=paste(FILESf,collapse=","),v=T,rtwindow=30,o="combined.peakml",combination="set",ppm=5, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| Combine 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 {
v: true
rtwindow: 30.0
ppm: 5.0
labels: []
combination: set
o: null
label: null
h: false
i: [-o, combined.peakml]
}
Loading:
- -o
java.io.FileNotFoundException: -o (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.Combine.main(Combine.java:338)
> mzmatch.ipeak.filter.NoiseFilter (i="combined.peakml",o="combined_noisef.peakml",v=T,codadw=0.8, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| NoiseFilter 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 {
v: true
rejected: null
o: combined_noisef.peakml
codadw: 0.8
h: false
i: [combined.peakml]
}
[ERROR]: the input-file 'combined.peakml' does not exist.
> mzmatch.ipeak.filter.SimpleFilter(i="combined_noisef.peakml", o="combined_sfdet.peakml", mindetections=3, v=T, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| SimpleFilter 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 {
maxretentiontime: -1.0
n: -1
o: combined_sfdet.peakml
minmass: -1.0
h: false
i: [combined_noisef.peakml]
minscanid: -1.0
v: true
maxintensity: -1.0
mindetections: 3
ppm: 0.0
databases: []
rejected: null
minretentiontime: -1.0
annotations: []
maxscanid: -1.0
offset: 0
maxmass: -1.0
minintensity: -1.0
}
[ERROR]: the input-file 'combined_noisef.peakml' does not exist.
> mzmatch.ipeak.filter.SimpleFilter(i="combined_sfdet.peakml", o="combined_highintensity.peakml", minintensity=1000, v=T, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| SimpleFilter 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 {
maxretentiontime: -1.0
n: -1
o: combined_highintensity.peakml
minmass: -1.0
h: false
i: [combined_sfdet.peakml]
minscanid: -1.0
v: true
maxintensity: -1.0
mindetections: -1
ppm: 0.0
databases: []
rejected: null
minretentiontime: -1.0
annotations: []
maxscanid: -1.0
offset: 0
maxmass: -1.0
minintensity: 1000.0
}
[ERROR]: the input-file 'combined_sfdet.peakml' does not exist.
> PeakML.GapFiller(filename = "combined_highintensity.peakml", ionisation = "positive", Rawpath = NULL, outputfile = "highintensity_gapfilled.peakml", ppm = 0, rtwin = 0)
Error: XML content does not seem to be XML: 'combined_highintensity.peakml'
Timing stopped at: 0.02 0.02 0.04
Timing stopped at: 0.11 0.02 0.13
> mzmatch.ipeak.sort.RelatedPeaks (i="highintensity_gapfilled.peakml",v=T,o="mzMatch_output.peakml",basepeaks="mzMatch_basepeaks.peakml",ppm=3,rtwindow=30, JHeapSize=6000)
------------------------------------------------------
| 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 {
v: true
minrt: -1.0
rtwindow: 30.0
ppm: 3.0
basepeaks: mzMatch_basepeaks.peakml
o: mzMatch_output.peakml
h: false
i: highintensity_gapfilled.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)
> annot <- paste("relation.id,relation.ship,codadw,charge")
> mzmatch.ipeak.convert.ConvertToText (i="mzMatch_output.peakml",o="mzMATCHoutput.txt",v=T,annotations=annot, JHeapSize=6000)
------------------------------------------------------
| 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 {
v: true
databases: []
o: mzMATCHoutput.txt
annotations: [relation.id, relation.ship, codadw, charge]
h: false
i: [mzMatch_output.peakml]
}
[ERROR]: the input-file 'mzMatch_output.peakml' does not exist.
>
>
>
> # Processing finished! Now extracting chromatogram images for each peak.
> chromdir <- "chromatograms"
> dir.create(chromdir)
> PeakMLData <- PeakML.Read("mzMatch_output.peakml",Rawpath=NULL)
Error: XML content does not seem to be XML: 'mzMatch_output.peakml'
Timing stopped at: 0 0.02 0.01
> 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$peakDataMtx[hits[i],9] %in% sampleslist==TRUE){
+ points (rtlist[[i]], intslist[[i]], type="l", col=classnumbers[samplenumbers [i]])}}
+ par(fig=c(0,1,0,1))
+ lpos <- par("usr")[2]-(lw /(1-lw ))*(par("usr")[2]-par("usr")[1])
+ legend (lpos, par("usr")[4], text.col=unique(classnumbers[sampleslist]), unique(samplegroups[sampleslist]), cex=0.8,xpd=TRUE)
+ dev.off()}
Error: object 'peakIDlist' not found
I do not see any files created, but there are empty folders. There is only a text file named error.txt that has this in it:
java.io.FileNotFoundException: highintensity_gapfilled.peakml (The system cannot find the file specified)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(Unknown Source)
at java.io.FileInputStream.<init>(Unknown Source)
at mzmatch.ipeak.sort.RelatedPeaks.main(RelatedPeaks.java:257)
I am not sure what I doing wrong here, any help would be greatly appreciated.
Thanks,
Brad
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
During startup - Warning message:
class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
> setwd("U:/Research/Jaya/IDEOM_Test_Lite")
>
> library (rJava)
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)
Loading required package: xcms
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:rJava’:
anyDuplicated, duplicated, sort, unique
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘xcms’
The following objects are masked from ‘package:Biobase’:
phenoData, phenoData<-
Loading required package: XML
Loading required package: snow
Attaching package: ‘snow’
The following objects are masked from ‘package:BiocGenerics’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parApply, parCapply, parLapply, parRapply, parSapply
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster
Loading required package: caTools
Loading required package: bitops
Loading required package: tcltk
Loading required package: ptw
Loading required package: gplots
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowess
> mzmatch.init (6000)
C:/Users/BEvans/Documents/R/win-library/3.0/mzmatch.R/java/mzmatch.jar
>
> rawfiles <- dir (full.names=TRUE,pattern="\\.mzXML*",recursive=TRUE)
> outputfiles <- paste(sub(".mzXML*","",rawfiles),".peakml",sep="")
> for (i in 1:length(rawfiles)){xset <- xcmsSet(rawfiles[i], method='centWave', ppm=10, peakwidth=c(15,100), snthresh=10, prefilter=c(3,1000), integrate=1, mzdiff=0.001, verbose.columns=TRUE, fitgauss=FALSE, nSlaves=1)
+ PeakML.xcms.write.SingleMeasurement (xset=xset,filename=outputfiles[i],ionisation="positive",addscans=2,writeRejected=FALSE,ApodisationFilter=TRUE)}
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
missing values in 'row.names' are not allowed
>
> MainClasses <- dir ()
> dir.create ("combined_RSD_filtered")
> dir.create ("combined_RSD_rejected")
> dir.create ("combined")
> for (i in 1:length(MainClasses)){FILESf <- dir (MainClasses[i],full.names=TRUE,pattern="\\.peakml$",recursive=TRUE)
+ OUTPUTf <- paste ("combined/",MainClasses[i],".peakml",sep="")
+ if(length(FILESf)>0){mzmatch.ipeak.Combine (i=paste(FILESf,collapse=","),v=T,rtwindow=30,o=OUTPUTf,combination="set",ppm=5,label=paste(MainClasses[i],sep=""), JHeapSize=6000)
+ RSDf <- paste ("combined_RSD_filtered/",MainClasses[i],".peakml",sep="")
+ REJf <- paste ("combined_RSD_rejected/",MainClasses[i],".peakml",sep="")
+ if(length(FILESf)>1) mzmatch.ipeak.filter.RSDFilter(i=OUTPUTf,o=RSDf,rejected=REJf,rsd=0.8, JHeapSize=6000) else file.copy(OUTPUTf,RSDf)}}
> INPUTDIR <- "combined_RSD_filtered"
> FILESf <- dir (INPUTDIR,full.names=TRUE,pattern="\\.peakml$")
> mzmatch.ipeak.Combine(i=paste(FILESf,collapse=","),v=T,rtwindow=30,o="combined.peakml",combination="set",ppm=5, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| Combine 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 {
v: true
rtwindow: 30.0
ppm: 5.0
labels: []
combination: set
o: null
label: null
h: false
i: [-o, combined.peakml]
}
Loading:
- -o
java.io.FileNotFoundException: -o (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.Combine.main(Combine.java:338)
> mzmatch.ipeak.filter.NoiseFilter (i="combined.peakml",o="combined_noisef.peakml",v=T,codadw=0.8, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| NoiseFilter 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 {
v: true
rejected: null
o: combined_noisef.peakml
codadw: 0.8
h: false
i: [combined.peakml]
}
[ERROR]: the input-file 'combined.peakml' does not exist.
> mzmatch.ipeak.filter.SimpleFilter(i="combined_noisef.peakml", o="combined_sfdet.peakml", mindetections=3, v=T, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| SimpleFilter 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 {
maxretentiontime: -1.0
n: -1
o: combined_sfdet.peakml
minmass: -1.0
h: false
i: [combined_noisef.peakml]
minscanid: -1.0
v: true
maxintensity: -1.0
mindetections: 3
ppm: 0.0
databases: []
rejected: null
minretentiontime: -1.0
annotations: []
maxscanid: -1.0
offset: 0
maxmass: -1.0
minintensity: -1.0
}
[ERROR]: the input-file 'combined_noisef.peakml' does not exist.
> mzmatch.ipeak.filter.SimpleFilter(i="combined_sfdet.peakml", o="combined_highintensity.peakml", minintensity=1000, v=T, JHeapSize=6000)
------------------------------------------------------
| Copyright 2007-2009
| Groningen Bioinformatics Centre
| University of Groningen
|
| SimpleFilter 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 {
maxretentiontime: -1.0
n: -1
o: combined_highintensity.peakml
minmass: -1.0
h: false
i: [combined_sfdet.peakml]
minscanid: -1.0
v: true
maxintensity: -1.0
mindetections: -1
ppm: 0.0
databases: []
rejected: null
minretentiontime: -1.0
annotations: []
maxscanid: -1.0
offset: 0
maxmass: -1.0
minintensity: 1000.0
}
[ERROR]: the input-file 'combined_sfdet.peakml' does not exist.
> PeakML.GapFiller(filename = "combined_highintensity.peakml", ionisation = "positive", Rawpath = NULL, outputfile = "highintensity_gapfilled.peakml", ppm = 0, rtwin = 0)
Error: XML content does not seem to be XML: 'combined_highintensity.peakml'
Timing stopped at: 0.02 0.02 0.04
Timing stopped at: 0.11 0.02 0.13
> mzmatch.ipeak.sort.RelatedPeaks (i="highintensity_gapfilled.peakml",v=T,o="mzMatch_output.peakml",basepeaks="mzMatch_basepeaks.peakml",ppm=3,rtwindow=30, JHeapSize=6000)
------------------------------------------------------
| 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 {
v: true
minrt: -1.0
rtwindow: 30.0
ppm: 3.0
basepeaks: mzMatch_basepeaks.peakml
o: mzMatch_output.peakml
h: false
i: highintensity_gapfilled.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)
> annot <- paste("relation.id,relation.ship,codadw,charge")
> mzmatch.ipeak.convert.ConvertToText (i="mzMatch_output.peakml",o="mzMATCHoutput.txt",v=T,annotations=annot, JHeapSize=6000)
------------------------------------------------------
| 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 {
v: true
databases: []
o: mzMATCHoutput.txt
annotations: [relation.id, relation.ship, codadw, charge]
h: false
i: [mzMatch_output.peakml]
}
[ERROR]: the input-file 'mzMatch_output.peakml' does not exist.
>
>
>
> # Processing finished! Now extracting chromatogram images for each peak.
> chromdir <- "chromatograms"
> dir.create(chromdir)
> PeakMLData <- PeakML.Read("mzMatch_output.peakml",Rawpath=NULL)
Error: XML content does not seem to be XML: 'mzMatch_output.peakml'
Timing stopped at: 0 0.02 0.01
> 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
I do not see any files created, but there are empty folders. There is only a text file named error.txt that has this in it:
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)
I am not sure what I doing wrong here, any help would be greatly appreciated.
Thanks,
Brad
Darren
Mar 24, 2014, 11:43:50 PM3/24/14
to id...@googlegroups.com
Hi Brad,
It is difficult to say exactly what the problem is, but it appears that it cant find your raw files. Please check that you do have .mzXML files in the working directory and that none of these files have spaces or unusual characters in their names.
If they seem OK then perhaps try to open the mzXML files in another software (e.g. InsilicosViewer) to see that they are not corrupted.
Let us know how you get on.
cheers,
Darren
Brad Evans
Mar 26, 2014, 1:09:14 PM3/26/14
to id...@googlegroups.com
Darren,
Thanks, the files are indeed mzxml and there are centroided data in the files. I have the files in the same directory as IDEOM, in C:\ideom. The files do not have spaces or other characters in them. I think that it may be hanging up on the xcms portion because after peak detection I get this error:
Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
1441 Peaks.
positive
Error in rawdata[[which(names(rawdata) == ionisation)]] :
attempt to select less than one element
After that the other portions of the script run, but seem to be looking for files that xcms did not write.
Brad
Thanks, the files are indeed mzxml and there are centroided data in the files. I have the files in the same directory as IDEOM, in C:\ideom. The files do not have spaces or other characters in them. I think that it may be hanging up on the xcms portion because after peak detection I get this error:
Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
1441 Peaks.
positive
Error in rawdata[[which(names(rawdata) == ionisation)]] :
attempt to select less than one element
After that the other portions of the script run, but seem to be looking for files that xcms did not write.
Brad
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