Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_BCAP-N1-BDNA-1_B23KGCJLT4_1/1029_BCAP-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/076410126d616cf573dc20c7cf9808/.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/2e/076410126d616cf573dc20c7cf9808/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_BCAP-N1-BDNA-1_B23KGCJLT4_1/1029_BCAP-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BCAP-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BCAP-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCAP-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BCAP-N1-BDNA-1_B23KGCJLT4_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: 63590859 total, 38884 skipped (flags/unmapped)
Fragments: 31887871 total (31625096 tlen-paired, 2690 hash-paired, 254 singletons, 8612 discordant, 251219 orphans, 13853 too large [>5000 bp], 11596584 duplicates)
Reads: 64192650 total, 35923 skipped (flags/unmapped)
Fragments: 32182905 total (31949375 tlen-paired, 2581 hash-paired, 359 singletons, 6860 discordant, 223730 orphans, 7503 too large [>5000 bp], 11393319 duplicates)
Reads: 70149216 total, 62216 skipped (flags/unmapped)
Fragments: 35250955 total (34593477 tlen-paired, 2509 hash-paired, 305 singletons, 130219 discordant, 524445 orphans, 54920 too large [>5000 bp], 12786881 duplicates)
Reads: 58984189 total, 44500 skipped (flags/unmapped)
Fragments: 29567539 total (29344553 tlen-paired, 2698 hash-paired, 295 singletons, 9161 discordant, 210832 orphans, 7869 too large [>5000 bp], 10731200 duplicates)