Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B3PP-N1-BDNA-1_A23TNVNLT4_1/1241_B3PP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/5412a5f8c4d29aee7cbeb562b75ecf/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B3PP-N1-BDNA-1_A23TNVNLT4_1/1241_B3PP-N1-BDNA-1_A23TNVNLT4_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/6b/5412a5f8c4d29aee7cbeb562b75ecf/.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: 1241_B3PP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B3PP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B3PP-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B3PP-N1-BDNA-1_A23TNVNLT4_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: 71439740 total, 52102 skipped (flags/unmapped)
Fragments: 35943284 total (35416782 tlen-paired, 2466 hash-paired, 329 singletons, 9108 discordant, 514599 orphans, 7999 too large [>5000 bp], 15204637 duplicates)
Reads: 77011599 total, 44341 skipped (flags/unmapped)
Fragments: 38767955 total (38174892 tlen-paired, 2235 hash-paired, 503 singletons, 6510 discordant, 583815 orphans, 7833 too large [>5000 bp], 15967203 duplicates)
Reads: 76970868 total, 46200 skipped (flags/unmapped)
Fragments: 38739631 total (38151856 tlen-paired, 5557 hash-paired, 295 singletons, 7604 discordant, 574319 orphans, 10010 too large [>5000 bp], 16439130 duplicates)
Reads: 86970388 total, 87995 skipped (flags/unmapped)
Fragments: 44053885 total (42106965 tlen-paired, 3462 hash-paired, 355 singletons, 406585 discordant, 1536518 orphans, 155748 too large [>5000 bp], 18399313 duplicates)