SAIGE-GENE error

Question

[smyiz]

Hi,

I'm trying to run SAIGE-GENE for a genomic dataset on HPC. I created a sparseGRM, but I get some segmentation error when I run the step1:

*** caught segfault ***
address 0xc18c000, cause 'memory not mapped'
Segmentation fault (core dumped)

What I’ve eliminated as causes: Incorrect sample ID ordering or mismatch; Corrupted or improperly formatted sparse GRM matrix; Mismatch between phenotype, genotype, and GRM sample sets.

Does anyone have any experience running SAIGE/SAIGE-GENE? And any suggestion what may cause to this error? Thanks

[GenoMax]

Segfaults are related to memory, which is what part of the message is telling you. If you are running this job under a job scheduler make sure you ask for enough memory.