Question

Fastqc Exception Problem

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3.0 years ago

Maliha ▴ 30

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)

fastqc fastq • 3.4k views

ADD COMMENT • link updated 3.0 years ago by GenoMax 153k • written 3.0 years ago by Maliha ▴ 30

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

ADD REPLY • link 3.0 years ago by GenoMax 153k

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

ADD REPLY • link 3.0 years ago by Maliha ▴ 30

score 1 · Answer 1 · 2022-09-02

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3.0 years ago

GenoMax 153k

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

ADD COMMENT • link 3.0 years ago by GenoMax 153k

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

ADD REPLY • link 3.0 years ago by Maliha ▴ 30

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