Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_00C-N1-BDNA-1_A23MHW3LT4_1/1136_00C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/4a609fe892c287c480c92cf548bc62/.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/30/4a609fe892c287c480c92cf548bc62/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_00C-N1-BDNA-1_A23MHW3LT4_1/1136_00C-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] [W::hts_idx_load3] The index file is older than the data file: 1136_00C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_00C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_00C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_00C-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
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: 95736495 total, 64082 skipped (flags/unmapped)
Fragments: 48095612 total (47532692 tlen-paired, 4814 hash-paired, 541 singletons, 13929 discordant, 543636 orphans, 12683 too large [>5000 bp], 15622814 duplicates)
Reads: 91248206 total, 73555 skipped (flags/unmapped)
Fragments: 45842509 total (45275085 tlen-paired, 4649 hash-paired, 608 singletons, 20696 discordant, 541471 orphans, 15856 too large [>5000 bp], 15155098 duplicates)
Reads: 104749510 total, 68657 skipped (flags/unmapped)
Fragments: 52633351 total (51983337 tlen-paired, 7747 hash-paired, 589 singletons, 20826 discordant, 620852 orphans, 17796 too large [>5000 bp], 17474359 duplicates)
Reads: 106507225 total, 111051 skipped (flags/unmapped)
Fragments: 53748452 total (52029277 tlen-paired, 2606 hash-paired, 659 singletons, 331615 discordant, 1384295 orphans, 142112 too large [>5000 bp], 17794718 duplicates)