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