Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_01S-T1-TDNA-1_B23KFCWLT4_1/1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/b40b5e34192bfc2a718e371fa1f8c1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/b40b5e34192bfc2a718e371fa1f8c1/.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_01S-T1-TDNA-1_B23KFCWLT4_1/1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 1198481526 total, 2428669 skipped (flags/unmapped), 96960357 no site overlap
Fragments: 577201768 total (521111628 paired, 4397 singletons, 779104 discordant, 55306639 orphans)
Sites: 53092669 total, 12738411 with data, 6599941 output (depth>=10)
Reads: 1285998983 total, 2518529 skipped (flags/unmapped), 109485144 no site overlap
Fragments: 616070847 total (554023861 paired, 5230 singletons, 3900602 discordant, 58141154 orphans)
Sites: 53092669 total, 11798808 with data, 6219354 output (depth>=10)