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GenotypeGVCFs on X chromosome stuck in the process progression
I am processing 1000 WGS with gatk-22.214.171.124.
I ran HaplotypeCaller by sample and by chromosome and I took into account the sex status of my samples for the calling of the X chromosome (ploidy=1 for male, ploidy=2 for female).
This step executed successfully.
I then run CombineGVCFs by chromosome and this step also executed successfully.
I finally run GenotypeGVCFS by chromosome. It worked for the autosomes. But I have an issue with the X chromosome.
In fact, GenotypeGVCFs starts but get stuck at the first "ProgressMeter".
"12:35:56.093 INFO ProgressMeter - chrX:60999 29.8 1000 33.5"
As GenotypeGVCFs worked for all the autosomes, my interpretation is that maybe "dealing with differences of ploidy" would take much more memory and time.
Could it be that? If so, how can I handle it? If not, could you help me finding and solving my problem?