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GenotypeGVCFs processing stalls at position 999901

I'm running GenotypeGVCFs on about 50 samples, split by chromosome across several cluster nodes. I see that each sample, regardless of chromosome stalls at position 999901. This continues at 1999901, 2999901, and so on. More out of curiosity than anything, is there a straightforward explanation to this behavior?

Thanks!

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