Monday, April 1, 2019

fastqc -java.lang.OutOfMemoryError: Java heap space - Solved!

$fastqc filename.fastq
Started analysis of filename.fastq
Exception in thread "Thread-1" java.lang.OutOfMemoryError: Java heap space
    at uk.ac.babraham.FastQC.Modules.GCModel.GCModel.<init>(GCModel.java:69)
    at uk.ac.babraham.FastQC.Modules.PerSequenceGCContent.processSequence(PerSequenceGCContent.java:198)
    at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:88)
    at java.base/java.lang.Thread.run(Thread.java:844)


$ grep -n 'Xm' /home/prakki/sw/FastQC/fastqc
167:    unshift @java_args,"-Xmx${memory}m";
170:    unshift @java_args,'-Xmx250m';


$ vi /home/prakki/sw/FastQC/fastqc


Changed the 250m to 10g (depends on the RAM of your computer) in the line 170

$ fastqc filename.fastq
Started analysis of filename.fastq
Approx 5% complete for filename.fastq
Approx 10% complete for filename.fastq
Approx 15% complete for filename.fastq
Approx 20% complete for filename.fastq
Approx 25% complete for filename.fastq
Approx 30% complete for filename.fastq
Approx 35% complete for filename.fastq
Approx 40% complete for filename.fastq
Approx 45% complete for filename.fastq
Approx 50% complete for filename.fastq
Approx 55% complete for filename.fastq
Approx 60% complete for filename.fastq
Approx 65% complete for filename.fastq
Approx 70% complete for filename.fastq
Approx 75% complete for filename.fastq
Approx 80% complete for filename.fastq
Approx 85% complete for filename.fastq
Approx 90% complete for filename.fastq
Approx 95% complete for filename.fastq
Analysis complete for filename.fastq

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