Training in parallel causes error for loci "other" than HLA
Opened this issue · 2 comments
shubhamsaini commented
I am trying to train HIBAG models for loci other than HLA. Training the models in parallel causes the following error:
> hlaAllele(true_kir_types_train$sample.id, H1=true_kir_types_train$allele1, H2=true_kir_types_train$allele2, locus="any")
....
....
....
> hlaParallelAttrBagging(cl, train.allele, traingeno, nclassifier=10, auto.save="output.RData")
Calculating matching proportion:
Error in hlaCombineAllele(res, rv[[i]]) :
H1$pos.start == H2$pos.start is not TRUE
However, if I change the locus
parameter in hlaAllele
to some HLA gene, no error is thrown:
> hlaAllele(true_kir_types_train$sample.id, H1=true_kir_types_train$allele1, H2=true_kir_types_train$allele2, locus="A")
zhengxw-ab commented
hlaAllele(sample.id, H1, H2, max.resolution="", locus="any", assembly="auto",
locus.pos.start=NA_integer_, locus.pos.end=NA_integer_, prob=NULL,
na.rm=TRUE)
You will need to specify locus.pos.start
and locus.pos.end
.
shubhamsaini commented
Thanks @zhengxw-ab
But specifying the locus.pos.start
and locus.pos.end
still causes the same error.