I've got a complete data combining both positive and negative polarities. I've had problems in the past, but I've successfully gotten IDEOM to create an MZmatchoutput.txt for the positive polarity data by manually selecting each sub-directory for the step of running "XCMS to pick peaks and convert to peakML file(s)".
However, trying to do the same for the negative data is causing problems in Rgui. I've tried a few things, but eventually Rgui fails to locate one or more of the combined_* files nad runs aground.
I've put the text from the workspace into this post (see below), but I can't find or solve the problem.
I looked through the Rgui workspace and it directs me to the Javascript error (highlighted in yellow), but the error simply points out that a file cannot be found, offering no obvious solution.
Writing the results
> mzmatch.ipeak.filter.NoiseFilter (i="combined.peakml",o="combined_noisef.peakml",v=T,codadw=0.8, JHeapSize=4000) ------------------------------------------------------
| 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 {
rejected: null
codadw: 0.8
v: true
h: false
i: [combined.peakml]
o: combined_noisef.peakml
}
Loading 'combined.peakml'.
Calculating the signal-scores
Writing valid
> mzmatch.ipeak.filter.SimpleFilter(i="combined_noisef.peakml", o="combined_sfdet.peakml", mindetections=3, JHeapSize=4000)
> mzmatch.ipeak.filter.SimpleFilter(i="combined_sfdet.peakml", o="combined_highintensity.peakml", minintensity=1000, JHeapSize=4000)
> PeakML.GapFiller(filename = "combined_highintensity.peakml", ionisation = "detect", Rawpath = NULL, outputfile = "highintensity_gapfilled.peakml", ppm=5, rtwin = 0)Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\.\BLANK/BLK_01.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\.\BLANK/BLK_02.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\.\BLANK/BLK_03.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\.\BLANK/BLK_04.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\.\BLANK/BLK_5.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\.\BLANK/BLK_6.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\.\BLANK/BLK_7.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m01.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m02.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m03.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m04.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m05.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m06.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m07.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m08.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\Medium\./m09.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\QC\./QC_01.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\QC\./QC_2.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\QC\./QC_3.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\QC\./QC_4.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S1\./001.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S1\./002.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S1\./003.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S2\./004.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S2\./005.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S2\./006.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S3\./007.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S3\./008.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S3\./009.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S4\./010.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S4\./011.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S4\./012.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S5\./013.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S5\./014.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S5\./015.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S6\./016.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S6\./017.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S6\./018.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S7\./019.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S7\./020.mzXML
Raw data file can't be read from location': D:\LS_Celia\EZ20140428\Negative\S7\./021.mzXML
Raw data file can't be read from location': C:\Users\3125319\Desktop\EZ20140428\Negative\S8\./022.mzXML
Raw data file can't be read from location': C:\Users\3125319\Desktop\EZ20140428\Negative\S8\./023.mzXML
Raw data file can't be read from location': C:\Users\3125319\Desktop\EZ20140428\Negative\S8\./024.mzXML
Loading peakML file in memory (it can take some time, sorry)
Done in: 4.08 s
Extracting peak data from PeakMl file,
Peak data created in 7.65 s
Some of the raw data files are not accessible, we will not be able to fill in missing peaks. Please set "Rawpath" argument with location where files can be located
Error in PeakML.GapFiller(filename = "combined_highintensity.peakml", :
> mzmatch.ipeak.sort.RelatedPeaks (i="highintensity_gapfilled.peakml",v=T,o="mzMatch_output.peakml",basepeaks="mzMatch_basepeaks.peakml",ppm=3,rtwindow=6, JHeapSize=4000) ------------------------------------------------------
| 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)> annot <- paste("relation.id,relation.ship,codadw,charge")
> mzmatch.ipeak.convert.ConvertToText (i="mzMatch_output.peakml",o="mzMATCHoutput.txt",v=T,annotations=annot, JHeapSize=4000) ------------------------------------------------------