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Fastqc时报错

Fastqc时报错

作者: 所以suoyi | 来源:发表于2022-09-13 14:04 被阅读0次

    FastQC版本0.11.8

    出错命令行
    fastqc --extract -q -o fastqc_outdir fastq1 fastq2
    
    报错信息
    Exception in thread "Thread-1" java.lang.OutOfMemoryError: GC overhead limit exceeded
            at java.lang.String.toCharArray(String.java:2899)
    
    Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "Thread-1"
    Exception in thread "Thread-1" java.lang.OutOfMemoryError: Java heap space
            at java.lang.StringCoding$StringEncoder.encode(StringCoding.java:300)
            at java.lang.StringCoding.encode(StringCoding.java:344)
            at java.lang.StringCoding.encode(StringCoding.java:387)
            at java.lang.String.getBytes(String.java:958)
            at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:144)
            at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:178)
            at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
            at java.lang.Thread.run(Thread.java:748)
    Exception in thread "Thread-3" java.lang.OutOfMemoryError: GC overhead limit exceeded
            at java.lang.String.toCharArray(String.java:2899)
            at uk.ac.babraham.FastQC.Modules.PerSequenceQualityScores.processSequence(PerSequenceQualityScores.java:91)
            at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:88)
            at java.lang.Thread.run(Thread.java:748)
    Exception in thread "Thread-3" Exception in thread "Thread-3" java.lang.OutOfMemoryError: GC overhead limit exceeded
            at java.util.regex.Pattern$BnM.optimize(Pattern.java:5422)
            at java.util.regex.Pattern.compile(Pattern.java:1715)
            at java.util.regex.Pattern.<init>(Pattern.java:1352)
            at java.util.regex.Pattern.compile(Pattern.java:1028)
            at java.lang.String.replaceFirst(String.java:2178)
            at uk.ac.babraham.FastQC.Modules.BasicStats.processSequence(BasicStats.java:91)
            at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:88)
            at java.lang.Thread.run(Thread.java:748)
    
    修改
    fastqc --extract -q -t 10 -o fastqc_outdir fastq1 fastq2
    
     -t --threads    Specifies the number of files which can be processed
                        simultaneously.  Each thread will be allocated 250MB of
                        memory so you shouldn't run more threads than your
                        available memory will cope with, and not more than
                        6 threads on a 32 bit machine
    
    扩展
    https://github.com/s-andrews/FastQC/blob/master/fastqc
    

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