Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/363eba166e988cf76c8e6b793254d1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/29ca77f36ab860afe08eb798428957/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/ca4d20e41802bc8c33ea65523f74cb/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/7a5b825e0b2538511e427537624c8c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/7a5b825e0b2538511e427537624c8c/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled