Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Out of Memory issue with BAM files #24

Closed
MalhotraAnkit opened this issue Dec 10, 2018 · 2 comments
Closed

Out of Memory issue with BAM files #24

MalhotraAnkit opened this issue Dec 10, 2018 · 2 comments

Comments

@MalhotraAnkit
Copy link

Getting the following error on a merged oxford nanopore based BAM file. Suggestions ?

Exception in thread "Thread-1" java.lang.OutOfMemoryError: GC overhead limit exceeded
at uk.ac.babraham.FastQC.Modules.GCModel.GCModel.(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.lang.Thread.run(Thread.java:745)
@bioXiaoheng
Copy link

How big is your memory?

@s-andrews
Copy link
Owner

For memory issues (and nanopore can certainly trigger these if you have some very long reads) then you can try adding -t 2 (or even higher than 2) to force a higher memory allocation in fastqc.

@naumenko-sa naumenko-sa mentioned this issue Oct 22, 2019
Closed
jfy133 added a commit to nf-core/eager that referenced this issue Apr 8, 2020
@jfy133
Switch FASTQC to multicore
bc966a4 
In an attempt to close #378 following bcbio/bcbio-nextgen#2989 via s-andrews/FastQC#24
lordkev pushed a commit to lordkev/eager that referenced this issue May 6, 2020
@jfy133 @lordkev
Switch FASTQC to multicore
ef4f083 
In an attempt to close nf-core#378 following bcbio/bcbio-nextgen#2989 via s-andrews/FastQC#24
pontushojer added a commit to AfshinLab/BLR that referenced this issue Aug 17, 2020
@pontushojer
Update FASTQC command to run separate for reads and to use 2 threads.…
aede68a 
… This is to avoid running out of memory, see s-andrews/FastQC#24.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@s-andrews @MalhotraAnkit @bioXiaoheng