"Illegal instruction" error in BCF tools

Question

[raf.marcondes]

Hi all,

When I run the following command in in interactive session in my HPC system, it seems to run fine. I let it go for a minute or so, which it does without errors, and then kill it, because it's not appropriate to run such job in an interactive session.

But when I submit it as a batch job, it crashes with the following error within less than 10 secs of starting.

bcftools view -S ^outgrouplist -o tem.vcf thevcf_raw_24apr2020.vcf

25812 Illegal instruction     (core dumped) bcftools view -S ^outgrouplist -o tem.vcf thevcf_raw_24apr2020.vcf

I made sure that the output file doesn't already exist, because that's caused me errors in the past.

BCFTools 1.9.

Any thoughts?

Thanks!

[ATpoint]

Output of head outgrouplist?

[Kevin Blighe]

You may need to run it like this as part of the batch script:

echo `bcftools view -S ^outgrouplist -o tem.vcf thevcf_raw_24apr2020.vcf`

Those are backticks.