Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/80b617ca16a4110329479e6d557ce2/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_FZO-N1-BDNA-1_B23KGCJLT4_1/1029_FZO-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/f0/80b617ca16a4110329479e6d557ce2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_FZO-N1-BDNA-1_B23KGCJLT4_1/1029_FZO-N1-BDNA-1_B23KGCJLT4_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_FZO-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FZO-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FZO-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FZO-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: 106577557 total, 90231 skipped (flags/unmapped)
Fragments: 53434048 total (52990033 tlen-paired, 4254 hash-paired, 420 singletons, 24031 discordant, 415310 orphans, 17480 too large [>5000 bp], 22970170 duplicates)
Reads: 114713550 total, 81849 skipped (flags/unmapped)
Fragments: 57515300 total (57058736 tlen-paired, 4749 hash-paired, 625 singletons, 17750 discordant, 433440 orphans, 17583 too large [>5000 bp], 24308967 duplicates)
Reads: 114166640 total, 84958 skipped (flags/unmapped)
Fragments: 57255044 total (56754967 tlen-paired, 4899 hash-paired, 446 singletons, 21558 discordant, 473174 orphans, 22607 too large [>5000 bp], 24777862 duplicates)
Reads: 125918828 total, 120476 skipped (flags/unmapped)
Fragments: 63275086 total (62117180 tlen-paired, 3551 hash-paired, 483 singletons, 222751 discordant, 931121 orphans, 89892 too large [>5000 bp], 27383657 duplicates)