Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_MYJ-N1-BDNA-1_A23TY32LT4_1/1029_MYJ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_MYJ-N1-BDNA-1_A23TY32LT4_1/1029_MYJ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/6ce3daca0dbd2428c6a1580492143e/.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/b6/6ce3daca0dbd2428c6a1580492143e/.command.run
==> 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_MYJ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_MYJ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_MYJ-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_MYJ-N1-BDNA-1_A23TY32LT4_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: 75206841 total, 51444 skipped (flags/unmapped)
Fragments: 37682973 total (37436886 tlen-paired, 3366 hash-paired, 351 singletons, 10994 discordant, 231376 orphans, 10589 too large [>5000 bp], 13969922 duplicates)
Reads: 80988025 total, 44934 skipped (flags/unmapped)
Fragments: 40590198 total (40305153 tlen-paired, 4235 hash-paired, 272 singletons, 9769 discordant, 270769 orphans, 16868 too large [>5000 bp], 15127005 duplicates)
Reads: 80988350 total, 40555 skipped (flags/unmapped)
Fragments: 40587870 total (40335493 tlen-paired, 2596 hash-paired, 325 singletons, 7818 discordant, 241638 orphans, 7009 too large [>5000 bp], 14817082 duplicates)
Reads: 89137319 total, 79175 skipped (flags/unmapped)
Fragments: 44753318 total (44047608 tlen-paired, 2194 hash-paired, 330 singletons, 139524 discordant, 563662 orphans, 57750 too large [>5000 bp], 16663838 duplicates)