Good morning. I am using GATK3.8.1 to run HaplotypeCaller. I am doing so for 40 different samples. Attached is the error message. I used the nct option, "-nct option" and for some of the samples, I have obtained a g.vcf file and g.vcf.idx file, but for some, it crashes and the error message is shown. Should I re-run Haplotype Caller without the nct option or is there another solution? In addition, I have attached another image which shows that some samples have completed HaplotypeCaller successfully, but not the others. Please advise me. Thank you.
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