Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/dfff2f6be1b635a6c6168fae0de396/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/dfff2f6be1b635a6c6168fae0de396/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/aih-tih-sc-72469e-N1_B23T7FYLT4_1/aih-tih-sc-72469e-N1_B23T7FYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/aih-tih-sc-72469e-N1_B23T7FYLT4_1/aih-tih-sc-72469e-N1_B23T7FYLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-72469e-N1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-72469e-N1_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-72469e-N1_B23T7FYLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-72469e-N1_B23T7FYLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs