Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_dB3-N1-BDNA-1_A23TY32LT4_1/659_dB3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/507a9be8688cb951e8f62896d629b7/.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/3c/507a9be8688cb951e8f62896d629b7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_dB3-N1-BDNA-1_A23TY32LT4_1/659_dB3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
==> 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: 659_dB3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_dB3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dB3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dB3-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: 87060199 total, 64782 skipped (flags/unmapped)
Fragments: 43651728 total (43303408 tlen-paired, 4135 hash-paired, 326 singletons, 16402 discordant, 327457 orphans, 9872 too large [>5000 bp], 17204739 duplicates)
Reads: 95096969 total, 54887 skipped (flags/unmapped)
Fragments: 47681297 total (47322830 tlen-paired, 2922 hash-paired, 505 singletons, 11725 discordant, 343315 orphans, 11654 too large [>5000 bp], 18555529 duplicates)
Reads: 94360759 total, 59585 skipped (flags/unmapped)
Fragments: 47311806 total (46915099 tlen-paired, 5363 hash-paired, 319 singletons, 15010 discordant, 376015 orphans, 26948 too large [>5000 bp], 18780473 duplicates)
Reads: 104387504 total, 102935 skipped (flags/unmapped)
Fragments: 52453871 total (51476061 tlen-paired, 4178 hash-paired, 365 singletons, 192067 discordant, 781200 orphans, 79196 too large [>5000 bp], 20823705 duplicates)