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