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saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)
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ERROR: Reading nth marker failed. #110

Closed rmpb94 closed 1 year ago

rmpb94 commented 1 year ago

Hi,

I'm currently trying to run SAIGE-GENE+ for a set based test, but keep coming across this error: ERROR: Reading 24th marker failed

I am using vcf input, and the group file is ordered by chromosome position. Any idea what could be causing this error?

rmpb94 commented 1 year ago

After some further investigation, I think I have been able to work around this issue.

Instead of using .vcf files, I have make .bed, .bim, and .fam files. However, the group file identifiers now need to be in the format 1:12324:A:G not chr1:12324:A:G. Within the step 2 command the --chromflag also needs to be specified as--chrom=chr1

The documentation doesn't make this very clear. It might be worth adding more explicit detail about the file specifications for the different file inputs.

dmckean commented 3 months ago

Hi there. I'm seeing this under similar conditions. All error entries seem to refer the final variants in the affected groups (counter starts with zero). Output also mentions "Reach the end of the vcf file" in the preceding line of output.

Best I can tell is it's an error tripping up the VCF iterator used by the VcfClass::getOneMarker function. Switching formats away from VCF seems like the most straightforward workaround.