FastQC with java.lang.InternalError

Question

[zhangwel]

I had something wrong when runing the FastQC:

    fastqc SRR1552444.fastq.clean -o cleanfastqc/
Started analysis of SRR1552444.fastq.clean
Approx 5% complete for SRR1552444.fastq.clean
Approx 10% complete for SRR1552444.fastq.clean
Approx 15% complete for SRR1552444.fastq.clean
Approx 20% complete for SRR1552444.fastq.clean
Approx 25% complete for SRR1552444.fastq.clean
Approx 30% complete for SRR1552444.fastq.clean
Approx 35% complete for SRR1552444.fastq.clean
Approx 40% complete for SRR1552444.fastq.clean
Approx 45% complete for SRR1552444.fastq.clean
Approx 50% complete for SRR1552444.fastq.clean
Approx 55% complete for SRR1552444.fastq.clean
Approx 60% complete for SRR1552444.fastq.clean
Approx 65% complete for SRR1552444.fastq.clean
Approx 70% complete for SRR1552444.fastq.clean
Approx 75% complete for SRR1552444.fastq.clean
Approx 80% complete for SRR1552444.fastq.clean
Approx 85% complete for SRR1552444.fastq.clean
Approx 90% complete for SRR1552444.fastq.clean
Approx 95% complete for SRR1552444.fastq.clean
Analysis complete for SRR1552444.fastq.clean
Exception in thread "Thread-1" java.lang.InternalError: java.lang.reflect.InvocationTargetException
    at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
    at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
    at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
    at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
    at uk.ac.babraham.FastQC.Graphs.QualityBoxPlot.paint(QualityBoxPlot.java:88)
    at java.desktop/javax.swing.JComponent.print(JComponent.java:1220)
    at uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(AbstractQCModule.java:68)
    at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(PerBaseQualityScores.java:199)
    at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:131)
    at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:178)
    at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
    at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.reflect.InvocationTargetException
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
    ... 13 more
Caused by: java.lang.NullPointerException
    at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
    at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
    at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
    at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
    at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
    at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
    at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
    ... 18 more

How can I fix this?

Answer 1

[Pierre Lindenbaum]

as far as I understand, you have to install the package libfontconfig1 to fix this issue. https://github.com/AdoptOpenJDK/openjdk-docker/issues/75

[zhangwel]

It works，thanks very much！

[kyui]

yep, just run the command below, it will be ok.

• sudo apt-get update
• sudo apt-get install libfontconfig1