I am studying a non-model mouse species, and I am trying to produce a genomewide relatedness matrix using gcta64. I have a reference genome, but it is not yet annotated; therefore, the "chromosomes" are really scaffolds, and they number into the thousands. The error I receive when trying to produce the GRM is as follows:
Error: Line 1 of [file.bim] contains illegal chr number, please check
I tried to amend this by adding in an autosome-num option:
But so far my jobs (I'm submitting this command via a supercomputer) have all timed out. I submitted my newest request for 24 hours, but I fear that the job will time out because the options I have specified are incorrect.
Any suggestions with this would be greatly appreciated!