java - FastQC 无法处理 fastq 序列文件 - java.lang.NullPointerException

Question

我正在尝试在 RNA seq (.fastq) 上运行 fastqc，但遇到了尚未解决的问题:

Approx 5% complete for SRR5280293.fastq
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Approx 20% complete for SRR5280293.fastq
Approx 25% complete for SRR5280293.fastq
Approx 30% complete for SRR5280293.fastq
Approx 35% complete for SRR5280293.fastq
Approx 40% complete for SRR5280293.fastq
Approx 45% complete for SRR5280293.fastq
Approx 50% complete for SRR5280293.fastq
Approx 55% complete for SRR5280293.fastq
Approx 60% complete for SRR5280293.fastq
Approx 65% complete for SRR5280293.fastq
Approx 70% complete for SRR5280293.fastq
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Approx 80% complete for SRR5280293.fastq
Approx 85% complete for SRR5280293.fastq
Approx 90% complete for SRR5280293.fastq
Approx 95% complete for SRR5280293.fastq
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)

最后，我得到了一个空的 fastqc.zip 文件。没有 html 报告...我在 CentOS 7.3 上运行它，我的 java 版本是:

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)

有人可以帮助我吗？提前致谢!

Answer 1

这里有同样的问题，唯一成功的方法是删除我的 apt 版本(因为正如 mattbull 所说 here ，“来自 aptitude 的 FastQC 已经被破坏了很长时间”):

sudo apt-get purge fastqc

然后注销并登录您的实例以重置 PATH。

然后，在Anaconda中搜索0.11.8 FastQC版本，因为我们知道工作良好的jdk版本放在包中。

conda search -c bioconda fastqc

然后，安装它

conda install -c bioconda fastqc=0.11.8

至少这个错误对我来说消失了，我可以正常使用 FastQC。