Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BC9J-N1-BDNA-1_B23H2GYLT3_1/1029_BC9J-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/7222b52bc3d560634cb688f7de4d3e/.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/39/7222b52bc3d560634cb688f7de4d3e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BC9J-N1-BDNA-1_B23H2GYLT3_1/1029_BC9J-N1-BDNA-1_B23H2GYLT3_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_BC9J-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BC9J-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BC9J-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BC9J-N1-BDNA-1_B23H2GYLT3_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: 85221254 total, 83903 skipped (flags/unmapped)
Fragments: 42795409 total (42295923 tlen-paired, 14235 hash-paired, 6621 singletons, 9394 discordant, 469236 orphans, 11195 too large [>5000 bp], 9185209 duplicates)
Reads: 93221829 total, 68922 skipped (flags/unmapped)
Fragments: 46837630 total (46275035 tlen-paired, 13361 hash-paired, 7168 singletons, 6643 discordant, 535423 orphans, 10119 too large [>5000 bp], 10023635 duplicates)
Reads: 94030711 total, 71051 skipped (flags/unmapped)
Fragments: 47237979 total (46665401 tlen-paired, 16850 hash-paired, 7174 singletons, 9080 discordant, 539474 orphans, 15175 too large [>5000 bp], 10055777 duplicates)
Reads: 96563665 total, 121178 skipped (flags/unmapped)
Fragments: 48787829 total (47036540 tlen-paired, 15620 hash-paired, 7474 singletons, 340692 discordant, 1387503 orphans, 130903 too large [>5000 bp], 10270717 duplicates)