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Java misses head font #52548

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allysonFDSmtp opened this issue Dec 3, 2024 · 0 comments
Open

Java misses head font #52548

allysonFDSmtp opened this issue Dec 3, 2024 · 0 comments

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@allysonFDSmtp
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allysonFDSmtp commented Dec 3, 2024

Hi everyone,
Looks like there is still a problem with Java because when I try to process a fastqc into my env conda I have this error :

Failed to process file sample1_R1_001.fastq.gz
  java.lang.RuntimeException: Fontconfig head is null, check your fonts or fonts configuration
        at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1263)
        at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:221)
        at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:105)
        at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:696)
        at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:352)
        at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:309)
        at java.base/java.security.AccessController.doPrivileged(AccessController.java:319)
        at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:309)
        at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
        at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:55)
        at java.desktop/sun.font.PlatformFontInfo.createFontManager(PlatformFontInfo.java:37)
        at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:51)
        at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:242)
        at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:260)
        at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:862)
        at uk.ac.babraham.FastQC.Graphs.QualityBoxPlot.paint(QualityBoxPlot.java:88)
        at java.desktop/javax.swing.JComponent.print(JComponent.java:1274)
        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:1583)
       

I have those library in my env conda


openjdk                   17.0.11              h24d6bf4_0    conda-forge
fastqc                    0.11.7               hdfd78af_7    bioconda
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      2.001                hcb22688_0  
font-ttf-source-code-pro  2.030                hd3eb1b0_0  
font-ttf-ubuntu           0.83                 h8b1ccd4_0  
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-anaconda            1                    h8fa9717_0  
fonts-conda-ecosystem     1                    hd3eb1b0_0

Thank you for your help

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