Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/aed976a1aca0f00dbb8504cd5f65d2/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_Lx-N1-BDNA-1_B23KGCJLT4_1/659_Lx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  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/ca/aed976a1aca0f00dbb8504cd5f65d2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_Lx-N1-BDNA-1_B23KGCJLT4_1/659_Lx-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] The index file is older than the data file: 659_Lx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Lx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Lx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Lx-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: 80129667 total, 54691 skipped (flags/unmapped)
Fragments: 40147190 total (39897040 tlen-paired, 2638 hash-paired, 328 singletons, 12160 discordant, 235024 orphans, 7974 too large [>5000 bp], 15657352 duplicates)
Reads: 85509874 total, 45715 skipped (flags/unmapped)
Fragments: 42844328 total (42592364 tlen-paired, 2791 hash-paired, 420 singletons, 8582 discordant, 240171 orphans, 8047 too large [>5000 bp], 16402780 duplicates)
Reads: 95372284 total, 79755 skipped (flags/unmapped)
Fragments: 47870694 total (47179834 tlen-paired, 2540 hash-paired, 348 singletons, 131283 discordant, 556689 orphans, 54089 too large [>5000 bp], 18792982 duplicates)
Reads: 94720951 total, 51386 skipped (flags/unmapped)
Fragments: 47463951 total (47159222 tlen-paired, 5359 hash-paired, 337 singletons, 12655 discordant, 286378 orphans, 14189 too large [>5000 bp], 18627640 duplicates)