Error in GATK BaseRecalibrator
I am trying to run gatk base recaliberator but keep getting this error
I have tried samtools quickcheck on my bam but there was no output (assuming it means no error) The BAM is 11gb. I have run many samples before using the same command but this one is really confusing me. The command I use-
singularity exec docker://broadinstitute/gatk:4.4.0.0 gatk BaseRecalibrator --intervals $intervals --interval-padding 100 -I ${ID}_P_markdup.bam -R $hg38 --known-sites $mills --known-sites $phase --known-sites $dbsnp -O ${ID}_P_recal_data.table --tmp-dir $tmp
Please help figuring out the issue.
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