Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_29V-N1-BDNA-1_A23MHW3LT4_1/1136_29V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/95839b3a7109ef2a2a06b04736ea49/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_29V-N1-BDNA-1_A23MHW3LT4_1/1136_29V-N1-BDNA-1_A23MHW3LT4_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/cb/95839b3a7109ef2a2a06b04736ea49/.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: 1136_29V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_29V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_29V-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_29V-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: 82966911 total, 62370 skipped (flags/unmapped)
Fragments: 41662958 total (41197303 tlen-paired, 3265 hash-paired, 487 singletons, 18847 discordant, 443056 orphans, 11084 too large [>5000 bp], 14041858 duplicates)
Reads: 89084723 total, 55528 skipped (flags/unmapped)
Fragments: 44730730 total (44256411 tlen-paired, 2943 hash-paired, 563 singletons, 13095 discordant, 457718 orphans, 13008 too large [>5000 bp], 14768067 duplicates)
Reads: 97823135 total, 97060 skipped (flags/unmapped)
Fragments: 49316666 total (47913627 tlen-paired, 2380 hash-paired, 497 singletons, 270606 discordant, 1129556 orphans, 111398 too large [>5000 bp], 16692320 duplicates)
Reads: 96913656 total, 61716 skipped (flags/unmapped)
Fragments: 48665836 total (48122682 tlen-paired, 3650 hash-paired, 464 singletons, 19012 discordant, 520028 orphans, 20380 too large [>5000 bp], 16497052 duplicates)