QC_raw_data , QC_clean_data fails to generate output: {sample}_{read}_fastqc.html
alakob opened this issue · 2 comments
hh-yoda-11-01.ebi.ac.uk> cat QC_clean_data_701_S8_L001_pR1.log QC_clean_data_701_S8_L001_pR2.log QC_clean_data_701_S8_L001_uR1.log QC_clean_data_701_S8_L001_uR2.log QC_raw_data_701_S8_L001_R1.log QC_raw_data_701_S8_L001_R2.log
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:251)
at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
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:1221)
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.(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:844)
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:488)
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:1288)
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:765)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:440)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:385)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 18 more
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:251)
at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
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:1221)
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.(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:844)
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:488)
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:1288)
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:765)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:440)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:385)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 18 more
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:251)
at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
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:1221)
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.(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:844)
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:488)
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:1288)
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:765)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:440)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:385)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 18 more
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:251)
at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
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:1221)
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.(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:844)
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:488)
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:1288)
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:765)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:440)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:385)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 18 more
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:251)
at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
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:1221)
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.(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:844)
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:488)
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:1288)
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:765)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:440)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:385)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 18 more
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:251)
at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:264)
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:1221)
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.(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:844)
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:488)
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:1288)
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:765)
at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:440)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.font.SunFontManager.(SunFontManager.java:385)
at java.desktop/sun.awt.FcFontManager.(FcFontManager.java:35)
at java.desktop/sun.awt.X11FontManager.(X11FontManager.java:56)
... 18 more
Just so I can troubleshoot it, can you add the output of bash jovian -v for the version? And are you working with public data, if so which? Then I can try to recreate the problem.
Just as a first hunch, I've seen these errors before when performing multiple consecutive analyses in the same folder without cleaning up the previous analysis (either via --clean or --archive). Could you do a bash jovian --clean (NB you'll remove all generated data), try again and see if the problem still occurs?
@alakob Did that solve the issue? Please let us know because I'm doing a cleanup of open issues and otherwise I'll close it.