Problems running "MZmatch to combine data and annotate related peaks"

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Lucas Schwartzenberg

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May 28, 2014, 8:35:20 AM5/28/14
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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)

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

Lucas Schwartzenberg

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May 28, 2014, 8:48:31 AM5/28/14
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PS: reading through some of the other posts on this subject, I have checked the following:
- The directory path to this data, or the filesnames themsleves do not contain any spaces.
- the sub-directories (inside the main Negative polarity file) contain *.MZxml files and for each one there is a matching *.peakML file (
with one exception, with will be cleared up by the time I post this).

Andris Jankevics

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May 28, 2014, 9:58:22 AM5/28/14
to Lucas Schwartzenberg, Ideom

On Wed, May 28, 2014 at 1:48 PM, Lucas Schwartzenberg <lucass...@gmail.com> wrote:
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


Hi Lucas, error message of the GapFiller function indicates that mzmatch can't locate all mzXML files witing subfolders. Why some of you data files were on "D" drive and some on "C"?  Did you copied data files from one folder to another? You can specify other data folder using "Rawpath" argument of gapfiller function. 


That's why function fails and other step of data processing pipe-line as well. 

Andris

Vincent Bonifay

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May 28, 2014, 6:20:44 PM5/28/14
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Hi Lucas

I had the same problem at some point. As Andris mentioned you probably moved the files. I did the centewave method for the xcms part on one computer. Then i copied everything to a different computer and finished the mzMatch process on it. This is where i got the error, because gapfiller could not find the mzXML file which were associated to the peakML files.

Lucas Schwartzenberg

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Jun 17, 2014, 9:59:12 AM6/17/14
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The advice posted in this thread has helped me ahead. Thank you for your time.


On Wednesday, 28 May 2014 14:35:20 UTC+2, Lucas Schwartzenberg wrote:
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