Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/2ae6aec4eb5cc677198429a3faa9b5/.command.sh
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/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/4a/2ae6aec4eb5cc677198429a3faa9b5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0W2-T1-TDNA-1_A23KCGYLT4_1/1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0W2-T1-TDNA-1_A23KCGYLT4_1/1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-T1-TDNA-1_A23KCGYLT4_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
Reads: 214215279 total, 2023689 skipped (flags/unmapped)
Fragments: 107260859 total (104087283 tlen-paired, 159796 hash-paired, 1181 singletons, 380388 discordant, 2632211 orphans, 151632 too large [>5000 bp], 54835132 duplicates)
Reads: 236831598 total, 1559265 skipped (flags/unmapped)
Fragments: 118569349 total (116098001 tlen-paired, 137083 hash-paired, 1204 singletons, 164652 discordant, 2168409 orphans, 151624 too large [>5000 bp], 62239266 duplicates)
Reads: 246800120 total, 1921732 skipped (flags/unmapped)
Fragments: 123561536 total (120524833 tlen-paired, 172146 hash-paired, 1085 singletons, 302709 discordant, 2560763 orphans, 158582 too large [>5000 bp], 65686580 duplicates)
Reads: 260176032 total, 2131202 skipped (flags/unmapped)
Fragments: 130274579 total (126576457 tlen-paired, 188080 hash-paired, 1459 singletons, 495528 discordant, 3013055 orphans, 255093 too large [>5000 bp], 69053675 duplicates)