MuSE sump: Segmentation fault (core dumped)

Question

[Marie]

Hi all,

I'm running MuSE within a Snakemake pipeline. The MuSE call step completed successfully, but the subsequent MuSE sump step fails with the following error:

Segmentation fault (core dumped)

To debug, I have already

• Verified that the input file exists and is correctly formatted.
• Reduced the number of cores to 1 (using -n 1).
• Ensured that the MuSE call step generated a valid output.

Here’s the command used in my Snakemake rule:

MuSE sump -I {input} -O {output.vcf} -E -n {threads} 2>> {log}

Has anyone encountered this issue before or found a possible solution? Any help would be appreciated!

[Arup Ghosh]

Segmentation faults generally suggest memory limit-related issues. Can you share the log entries for MuSE sump?

Also, you can increase the memory for the process and re-run the pipeline.