Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_L3X-N1-BDNA-1_A23MHW3LT4_1/1029_L3X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/ea3815204370ae791d79ed41bf3cd0/.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/27/ea3815204370ae791d79ed41bf3cd0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_L3X-N1-BDNA-1_A23MHW3LT4_1/1029_L3X-N1-BDNA-1_A23MHW3LT4_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_L3X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_L3X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_L3X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_L3X-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 74634294 total, 65081 skipped (flags/unmapped)
Fragments: 37560953 total (36970366 tlen-paired, 4553 hash-paired, 434 singletons, 10823 discordant, 574777 orphans, 11259 too large [>5000 bp], 14323105 duplicates)
Reads: 79294782 total, 55171 skipped (flags/unmapped)
Fragments: 39915931 total (39286930 tlen-paired, 3294 hash-paired, 494 singletons, 7758 discordant, 617455 orphans, 12849 too large [>5000 bp], 14764981 duplicates)
Reads: 85788342 total, 59211 skipped (flags/unmapped)
Fragments: 43183334 total (42493877 tlen-paired, 8750 hash-paired, 420 singletons, 10456 discordant, 669831 orphans, 16357 too large [>5000 bp], 16458691 duplicates)
Reads: 88660553 total, 101745 skipped (flags/unmapped)
Fragments: 44950383 total (42835846 tlen-paired, 3043 hash-paired, 466 singletons, 423894 discordant, 1687134 orphans, 172821 too large [>5000 bp], 16901257 duplicates)