Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_FRC-N1-BDNA-1_B23KGCJLT4_1/1029_FRC-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/b998ed2cf3b63749b2262e9b1a6989/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_FRC-N1-BDNA-1_B23KGCJLT4_1/1029_FRC-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  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/d3/b998ed2cf3b63749b2262e9b1a6989/.command.run
==> 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_FRC-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FRC-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FRC-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FRC-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: 74008426 total, 55159 skipped (flags/unmapped)
Fragments: 37088008 total (36825333 tlen-paired, 3338 hash-paired, 430 singletons, 14178 discordant, 244729 orphans, 11205 too large [>5000 bp], 14884724 duplicates)
Reads: 78895141 total, 45333 skipped (flags/unmapped)
Fragments: 39540517 total (39278422 tlen-paired, 2104 hash-paired, 475 singletons, 10037 discordant, 249479 orphans, 9364 too large [>5000 bp], 15469095 duplicates)
Reads: 78850430 total, 50876 skipped (flags/unmapped)
Fragments: 39522082 total (39214397 tlen-paired, 2897 hash-paired, 357 singletons, 12250 discordant, 292181 orphans, 23964 too large [>5000 bp], 15901843 duplicates)
Reads: 86721006 total, 78915 skipped (flags/unmapped)
Fragments: 43539635 total (42854716 tlen-paired, 2558 hash-paired, 417 singletons, 131884 discordant, 550060 orphans, 56649 too large [>5000 bp], 17537764 duplicates)