Jonathon LeFaive
Jonathon LeFaive
Can you provide the first few records in your BED file?
I suspect you need to use the `chr` prefix in the BED file (eg, `chr1 `) since you are using build 38. If that doesn't fix it, I can look...
Ok, I'll look into this further. It will likely take a few weeks for me to get to it though. Are you able to exclude options like this from your...
Is the timestamp on the eigr file recent? Can you check that you are not low on RAM and using swap?
Sorry, I was actually looking for the modification timestamp. I'm trying assess whether the reml step is still running and making progress. Is there anything informative in the stderr output?
Hmm... that is way too much memory for 47,000 individuals. Seems like a bug. Can you try the latest pre-release https://github.com/statgen/EPACTS/releases or the latest from the develop branch?
I believe that the Minimac3 file format will allow for missing date and Minimac4 should support the older format. You can use `Minimac3 --processReference` to convert your vcf file. I'm...
I'm guessing you need to replace `DISEASE` with the column name of your phenotype.
Can you provide the first line of your ped file `head -n1 PPP.ped` and the full log output from your failed run? Does the vcf file and ped file contain...
No, subsetting the VCF is not necessary. I'm not sure what's going on. Can you test with `--vcf data/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --ped data/1000G_dummy_pheno.ped`? If it runs with the test data, then my...