A fatal error has been detected by the Java Runtime Environment

[mick42-star]

Hi, I was running fastqc on my computer and there is more than 200G left. I also run ulimit -c unlimited. But this problem still exists.

fastqc Jag1-6_S6_L001_R1_001.fastq.gz --dir ./
application/gzip
Started analysis of Jag1-6_S6_L001_R1_001.fastq.gz
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Analysis complete for Jag1-6_S6_L001_R1_001.fastq.gz

A fatal error has been detected by the Java Runtime Environment:

SIGILL (0x4) at pc=0x0000000102f4efc8, pid=26053, tid=28931

JRE version: OpenJDK Runtime Environment Homebrew (21.0.1) (build 21.0.1)

Java VM: OpenJDK 64-Bit Server VM Homebrew (21.0.1, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, bsd-aarch64)

Problematic frame:

C [libawt.dylib+0x2efc8] fillAAPgram+0x3e0

No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

An error report file with more information is saved as:

/Users/Desktop/running/hs_err_pid26053.log

[96.228s][warning][os] Loading hsdis library failed

If you would like to submit a bug report, please visit:

https://github.com/Homebrew/homebrew-core/issues

The crash happened outside the Java Virtual Machine in native code.

See problematic frame for where to report the bug.

zsh: abort fastqc Jag1-6_S6_L001_R1_001.fastq.gz --dir ./

[s-andrews]

That looks like a crash in one of the system libraries on your machine. Specifically in libawt which is a library which draws graphical interfaces. It could be that the library file itself is corrupt, or if could be a problem with the library which might be fixable if you update to a newer version. You appear to be using the Homebrew version of the library so you could try just reinstalling the java package from there:

https://superuser.com/questions/324980/how-do-you-re-install-a-package-with-homebrew-mac, or you could try updating to the latest release if you're not using that already.

https://osxdaily.com/2021/02/13/how-update-homebrew-mac/

In either case this isn't a bug in fastqc, nor even in the java runtime environment, so the fix must be upstream of our code I'm afraid.

[mick42-star]

That looks like a crash in one of the system libraries on your machine. Specifically in libawt which is a library which draws graphical interfaces. It could be that the library file itself is corrupt, or if could be a problem with the library which might be fixable if you update to a newer version. You appear to be using the Homebrew version of the library so you could try just reinstalling the java package from there:

https://superuser.com/questions/324980/how-do-you-re-install-a-package-with-homebrew-mac, or you could try updating to the latest release if you're not using that already.

https://osxdaily.com/2021/02/13/how-update-homebrew-mac/

In either case this isn't a bug in fastqc, nor even in the java runtime environment, so the fix must be upstream of our code I'm afraid.

Hi Andrew, thanks for your reply, I updated homebrew and reinstalled fastqc, but still doesn't work. So I installed conda version of fastqc and it works well.

[DENGARDEN]

I have the same issue with macOS (macOS 14.2.1 23C71 arm64) with fastqc version v0.12.1
I solved it via ubuntu server working on fastqc v.0.11.9.

[leowill01]

i was having same issue with the homebrew install of fastqc 0.12.1 on my mac studio m2 ultra.
thought it was because of apple silicon compatibility, but can confirm the conda installation of fastqc 0.12.1 works again.