FastQC fails to process fastq sequence file - java.lang.NullPointerException

Question

I am trying to run fastqc on RNA seq (.fastq) and I get this issue that I haven't managed to fix yet:

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Analysis complete for SRR5280293.fastq
Failed to process file SRR5280293.fastq
java.lang.NullPointerException
    at sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1264)
    at sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:219)
    at sun.awt.FontConfiguration.init(FontConfiguration.java:107)
    at sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:774)
    at sun.font.SunFontManager$2.run(SunFontManager.java:431)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.font.SunFontManager.<init>(SunFontManager.java:376)
    at sun.awt.FcFontManager.<init>(FcFontManager.java:35)
    at sun.awt.X11FontManager.<init>(X11FontManager.java:57)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at java.lang.Class.newInstance(Class.java:442)
    at sun.font.FontManagerFactory$1.run(FontManagerFactory.java:83)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
    at sun.font.SunFontManager.getInstance(SunFontManager.java:250)
    at sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
    at sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:855)
    at uk.ac.babraham.FastQC.Graphs.QualityBoxPlot.paint(QualityBoxPlot.java:88)
    at javax.swing.JComponent.print(JComponent.java:1202)
    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:155)
    at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
    at java.lang.Thread.run(Thread.java:748)

In the end, I get a fastqc.zip file which is empty. No html report... I run it on CentOS 7.3 and my java version is:

openjdk version "1.8.0_161"
OpenJDK Runtime Environment (build 1.8.0_161-b14)
OpenJDK 64-Bit Server VM (build 25.161-b14, mixed mode)

Can someone help me? Thanks in advance!

This seems to be an issue with your java installation. Take a look at the solutions listed [here](https://stackoverflow.com/questions/30626136/cannot-load-font-in-jre-8) and hopefully, the issue should get resolved. — pd321, Feb 22 '18 at 04:20

score 1 · Answer 1 · answered Mar 10 '20 at 06:01

Had the same problem here, the only successful way were to remove my apt version (because as mattbull says here, "FastQC from aptitude has been broken for ages") with:

sudo apt-get purge fastqc

And then logout and login to your instance to reset the PATH.

Then, search the 0.11.8 FastQC version in Anaconda because we know that the good working jdk version is put in the package.

conda search -c bioconda fastqc

Then, install it with

conda install -c bioconda fastqc=0.11.8

And at least the bug disappear for me only with this and I can use normally FastQC.

FastQC fails to process fastq sequence file - java.lang.NullPointerException

1 Answers1