About fastqc of Biocontainers and Java

Overview

A stack trace may appear on certain versions of fastqc in BioContainers Community.

I used

quay.io/biocontainers/fastqc:0.11.7--5

In addition, there are times when a stack trace appears with a tool that uses Java.

Conclusion

Use quay.io/biocontainers/fastqc:0.11.8--1. It seems that later versions may be used.

Also, some Java-based tools sometimes produce stack traces around the shared library. In that case, if you can switch to a new version, switch to it. If you can't do that, try creating an issue.

log

quay.io/biocontainers/fastqc:0.11.7--5

When you do this

Analysis complete for SRR1812671.fastq
Exception in thread "Thread-2" java.lang.UnsatisfiedLinkError: /usr/local/jre/lib/amd64/libfontmanager.so: libfreetype.so.6: cannot open shared object file: No such file or directory
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1845)
        at java.lang.Runtime.loadLibrary0(Runtime.java:870)
        at java.lang.System.loadLibrary(System.java:1122)
        at sun.font.FontManagerNativeLibrary$1.run(FontManagerNativeLibrary.java:61)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.font.FontManagerNativeLibrary.<clinit>(FontManagerNativeLibrary.java:32)
        at sun.font.SunFontManager$1.run(SunFontManager.java:361)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.font.SunFontManager.<clinit>(SunFontManager.java:357)
        at sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
        at sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
        at uk.ac.babraham.FastQC.Graphs.QualityBoxPlot.paint(QualityBoxPlot.java:88)
        at javax.swing.JComponent.print(JComponent.java:1203)
        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.lang.Thread.run(Thread.java:745)
Analysis complete for SRR1812639.fastq
Exception in thread "Thread-1" java.lang.NoClassDefFoundError: Could not initialize class sun.font.SunFontManager
        at sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
        at sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
        at uk.ac.babraham.FastQC.Graphs.QualityBoxPlot.paint(QualityBoxPlot.java:88)
        at javax.swing.JComponent.print(JComponent.java:1203)
        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.lang.Thread.run(Thread.java:745)

I get this error.

When I used the new version, the error disappeared.

quay.io/biocontainers/fastqc:0.11.8--1