The re-calibration (BQSR) step didn't finish. I will use the on-the-fly capacity in HaplotypeCaller (HC) to apply the BQSR.
I am also trying to use the g.vcf pipeline for the first time. It is not really necessary but I want to see what the output is and wanted to give it a shot. I specifically want to see if it gives me allele depth in positions that are snps in one sample and not the other. This is important for the downstream analysis.
NOTES: "When running in `-ERC GVCF` or `-ERC BP_RESOLUTION` modes, the emitting and calling confidence thresholds are automatically set to 0. This cannot be overridden by the command line. The thresholds can be set manually to the desired levels in the next step of the workflow (GenotypeGVCFs)"
I knew I was missing something when I couldn't find how to parallelize GATK. Following the instructions and suggestions here, I added the -nct 8 option to the PrintReads function it greatly increased the speed. I then submitted a HC function (on the new bam) with -nct 4 and it is running fast too.