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Old 03-18-2012, 09:30 AM   #1
fatrabbit
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Location: US

Join Date: Mar 2010
Posts: 7
Unhappy FluxSimulator error model

Hi,

I'm trying to use an error model for FluxSimulator-1.0-RC5 to generate reads with error. The read length I need is 100, so I can not use the default error model. Does anyone can give me an example for the error model file which suitable for the latest version? or let me knew the format of err file. Also, it looks that the FluxSimulator needs a GZIP file now.

I used the error model file which worked for a very old version of FluxSimulator one year before, but it doesn't work now, and gave me the following error message now:

[INFO] Reading error model /home/experiments/err100.err.gz
[ERROR] Unable to load error model : : only whitespace content allowed before start tag and not # (position: START_DOCUMENT seen \n#... @1:1)
com.thoughtworks.xstream.io.StreamException: : only whitespace content allowed before start tag and not # (position: START_DOCUMENT seen \n#... @1:1)
at com.thoughtworks.xstream.io.xml.XppReader.pullNextEvent(XppReader.java:67)
at com.thoughtworks.xstream.io.xml.AbstractPullReader.readRealEvent(AbstractPullReader.java:126)
at com.thoughtworks.xstream.io.xml.AbstractPullReader.readEvent(AbstractPullReader.java:119)
at com.thoughtworks.xstream.io.xml.AbstractPullReader.move(AbstractPullReader.java:98)
at com.thoughtworks.xstream.io.xml.AbstractPullReader.moveDown(AbstractPullReader.java:83)
at com.thoughtworks.xstream.io.xml.XppReader.<init>(XppReader.java:37)
at com.thoughtworks.xstream.io.xml.XppDriver.createReader(XppDriver.java:30)
at com.thoughtworks.xstream.io.xml.XppDriver.createReader(XppDriver.java:34)
at com.thoughtworks.xstream.XStream.fromXML(XStream.java:789)
at fbi.genome.sequencing.rnaseq.simulation.error.MarkovErrorModel.loadErrorModel(MarkovErrorModel.java:325)
at fbi.genome.sequencing.rnaseq.simulation.Sequencer.loadErrors(Sequencer.java:208)
at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:306)
at fbi.genome.sequencing.rnaseq.simulation.SimulationPipeline.call(SimulationPipeline.java:32)
at fbi.commons.flux.Flux.main(Flux.java:168)
Caused by: org.xmlpull.v1.XmlPullParserException: only whitespace content allowed before start tag and not # (position: START_DOCUMENT seen \n#... @2:2)
at org.xmlpull.mxp1.MXParser.parseProlog(MXParser.java:1519)
at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1395)
at org.xmlpull.mxp1.MXParser.next(MXParser.java:1093)
at com.thoughtworks.xstream.io.xml.XppReader.pullNextEvent(XppReader.java:52)
... 13 more
[ERROR] Unable to load error model : : only whitespace content allowed before start tag and not # (position: START_DOCUMENT seen \n#... @1:1)

Thanks,

Last edited by fatrabbit; 03-18-2012 at 09:35 AM.
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Old 03-19-2012, 01:52 PM   #2
fatrabbit
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If anybody knows it, please help me............Thanks
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Old 03-27-2012, 07:33 AM   #3
steven
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Just in case, don't forget to ask the author: micha at sammeth dot net
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