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




Recommended Posts

About fastqc of Biocontainers and Java
About an instance of java
[Java] About String and StringBuilder
Advantages and disadvantages of Java
About Java Packages and imports
[Java] About Objects.equals () and Review of String comparisons (== and equals)
About Java static and non-static methods
About Lambda, Stream, LocalDate of Java8
[Java beginner] About abstraction and interface
[Java] Set structure of collection class (about HashSet and TreeSet)
[Java] Judgment of identity and equivalence
About removeAll and retainAll of ArrayList
About Java primitive types and reference types
This and that about Base64 (Java)
[Java] I thought about the merits and uses of "interface"
About miscellaneous impressions of "Testing Java Microservices" and Consumer Driven Contract
After 3 months of Java and Spring training
About the operation of next () and nextLine ()
[Java] Inheritance and structure of HttpServlet class
[About JDBC that connects Java and SQL]
[Java / Swift] Comparison of Java Interface and Swift Protocol
[Java beginner] About initialization of multidimensional array
[Basic knowledge of Java] About type conversion
About the mechanism of the Web and HTTP
Summary of Java Math.random and import (Calendar)
[Java] Contents of Collection interface and List interface
Basics of java basics ② ~ if statement and switch statement ~
Discrimination of Enums in Java 7 and above
About Java interface
[Java] About Java 12 features
[Java] About arrays
About the classification and concept of Immutable / Mutable / Const / Variable of Java and Kotlin.
Something about java
Where about java
About Java features
About Java threads
[Java] About interface
About Java class
Java and JavaScript
About Java arrays
XXE and Java
About java inheritance
About interface, java interface
[Java] Overview of Java
About List [Java]
About java var
About Java literals
About Java commands
Think about the combination of Servlet and Ajax
About the description order of Java system properties
[Java] Personal summary of classes and methods (basic)
About Java data types (especially primitive types) and literals
[Java] The confusing part of String and StringBuilder
I compared the characteristics of Java and .NET
JAVA: Realizes generation and scanning of various barcodes
Basics of threads and Callable in Java [Beginner]
About call timing and arguments of addToBackStack method
[Java] Classification memo of compilation error and run-time error
About next () and nextLine () of the Scanner class
Java enables extraction of PDF text and images
About Java log output