Hi @WansonChoi and team, thank you for this helpful tool. I am using this pipeline with the T1DGC reference to impute HLA alleles for ~60k samples. I am performing this on a desktop with 32 GB memory and 4.29 GHz 6-core processor, using the options -mem 29g -mp 6 -nth 8. The software got to the point of Performing HLA imputation(exon3 / overlap: 5000) in about 2 hours, then was stuck there for 3 days. Would you be able to comment on whether this is normal, or what is the usual expected runtime for this many samples on such a machine?
I also got a warning initially that ~114k markers failed to lift down to hg18. Would that indicate the use of a different reference? Currently using hg19 which I believe is correct for the samples, and I tried different ones but CookHLA would give errors.
Hi @WansonChoi and team, thank you for this helpful tool. I am using this pipeline with the T1DGC reference to impute HLA alleles for ~60k samples. I am performing this on a desktop with 32 GB memory and 4.29 GHz 6-core processor, using the options
-mem 29g -mp 6 -nth 8. The software got to the point of Performing HLA imputation(exon3 / overlap: 5000) in about 2 hours, then was stuck there for 3 days. Would you be able to comment on whether this is normal, or what is the usual expected runtime for this many samples on such a machine?I also got a warning initially that ~114k markers failed to lift down to hg18. Would that indicate the use of a different reference? Currently using hg19 which I believe is correct for the samples, and I tried different ones but CookHLA would give errors.
Thanks in advance!