Jonathon LeFaive
Jonathon LeFaive
I would expect that to be normal if you have tens of thousands of samples. You can get an idea of progress by looking at the output directory. There will...
According to the log, it's stuck on matrix inversion, which I believe should be single threaded. What percentage of CPU and memory is the pEmmax process using?
6 days does seem too long for the reml step with 18,000 samples. I would still let the job run to see if it finishes before the time limit. In...
All of the variants in the results file have a MAC below the threshold. I suspect you will have valid p-values for variants with MAC > 3 and MAF >...
There are default min MAC (3) and min MAF (0.001) thresholds for the `epacts single` command. You can see them being passed down to pEmmax in the logs. Is this...
You should use the kinship matrix generated with the full VCF in both the full and LOF association tests. The kinship matrix is an input to the mixed-model for each...
This is a known issue for very large sample sizes. You need to increase `--printBuffer`. I would try `--printBuffer 2000000000`.
Reopening since this eventually needs to be fixed and may help others in the meantime.
It will likely take a while before someone can review this.
Thanks for reporting. Can you provide the command line options you used for generating the SAV files and what format fields are present in the files you are evaluating (e.g.,...