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Fastqc Exception Problem

Hello, I am running fastqc on Ubuntu 20.04.4 LTS. While doing that, after some time this error message is coming up-

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:89) at java.base/java.lang.Thread.run(Thread.java:829) enter image description here

fastqc fastq
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updated by GenoMax GenoMax • written by Maliha • Maliha

FastQC ran out of memory. Do you have a small amount of memory available? Are you using virtual machine?

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written by GenoMax GenoMax

I am not using virtual machine. I have dual boot of windows 10 and Ubuntu. How do I add memory in fastqc?

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written by Maliha • Maliha

1 answer

Try running fastqc -t 2 youfile. See if that works. This hack assigns more memory to FastQC.

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written by GenoMax GenoMax

Yes, I am booted into Ubuntu now. Ubuntu has 80GB memory in total and currently it has 68GB free memory left.

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written by Maliha • Maliha

You are referring to disk storage not RAM. Can you try the command I suggested above to see if the job works.

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written by GenoMax GenoMax

Thank you so much. This worked and the fastqc analysis has been completed.

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written by Maliha • Maliha

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