Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/a2e7d428cfac7b7bfb7c213480c688/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/a2e7d428cfac7b7bfb7c213480c688/.command.run
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/dbsnp138.snps.hg38.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_11H-T1-TDNA-1_B23KFCWLT4_1/1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_11H-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 763082458 total, 2663545 skipped (flags/unmapped), 63118875 no site overlap
Fragments: 362213758 total (333694227 paired, 3348 singletons, 1392053 discordant, 27124130 orphans)
Sites: 53092669 total, 9994095 with data, 4880668 output (depth>=10)
Reads: 802510377 total, 3103406 skipped (flags/unmapped), 68712911 no site overlap
Fragments: 380508574 total (349022403 paired, 2976 singletons, 1163083 discordant, 30320112 orphans)
Sites: 53092669 total, 11245177 with data, 5485863 output (depth>=10)