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I used BaseRecalibration and generated a bam file using PrintReads correctly along with .bai which was generated automatically. However, when I am trying to reduce the bam file using ReduceReads, I am getting the error below:
/bam_base_recalib/dedup_51769_R1_R2_RG_realigned_recal_reads.bam is malformed: Premature EOF; BinaryCodec in readmode; file: /bam_base_recalib/dedup_51769_R1_R2_RG_realigned_recal_reads.bam