Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_U86-N1-BDNA-1_A23MHW3LT4_1/1029_U86-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_U86-N1-BDNA-1_A23MHW3LT4_1/1029_U86-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/bbc7fc7220f8e6b6d08d84f9dbbc6c/.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/a5/bbc7fc7220f8e6b6d08d84f9dbbc6c/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_U86-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_U86-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_U86-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_U86-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: 81027997 total, 46789 skipped (flags/unmapped)
Fragments: 40698386 total (40244402 tlen-paired, 3102 hash-paired, 483 singletons, 12516 discordant, 437883 orphans, 11401 too large [>5000 bp], 12948147 duplicates)
Reads: 76401288 total, 52562 skipped (flags/unmapped)
Fragments: 38380298 total (37929202 tlen-paired, 2681 hash-paired, 516 singletons, 17871 discordant, 430028 orphans, 9337 too large [>5000 bp], 12516008 duplicates)
Reads: 88514057 total, 50334 skipped (flags/unmapped)
Fragments: 44461345 total (43954513 tlen-paired, 3320 hash-paired, 436 singletons, 17703 discordant, 485373 orphans, 13421 too large [>5000 bp], 14501110 duplicates)
Reads: 89857150 total, 79873 skipped (flags/unmapped)
Fragments: 45322086 total (43972300 tlen-paired, 2201 hash-paired, 449 singletons, 260282 discordant, 1086854 orphans, 110204 too large [>5000 bp], 14786551 duplicates)