Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_KR2-N1-BDNA-1_B23H2GYLT3_1/1029_KR2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/ab8d6f412040d68f732ab0cc744e19/.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/29/ab8d6f412040d68f732ab0cc744e19/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_KR2-N1-BDNA-1_B23H2GYLT3_1/1029_KR2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> 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: 1029_KR2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KR2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KR2-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KR2-N1-BDNA-1_B23H2GYLT3_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: 72272951 total, 61945 skipped (flags/unmapped)
Fragments: 36295048 total (35885721 tlen-paired, 9364 hash-paired, 6442 singletons, 6997 discordant, 386524 orphans, 6938 too large [>5000 bp], 8648360 duplicates)
Reads: 72610195 total, 53161 skipped (flags/unmapped)
Fragments: 36477788 total (36041740 tlen-paired, 9108 hash-paired, 6402 singletons, 6382 discordant, 414156 orphans, 11008 too large [>5000 bp], 8592820 duplicates)
Reads: 78835718 total, 56640 skipped (flags/unmapped)
Fragments: 39608962 total (39139047 tlen-paired, 10132 hash-paired, 6734 singletons, 5181 discordant, 447868 orphans, 7878 too large [>5000 bp], 9348810 duplicates)
Reads: 81800478 total, 96665 skipped (flags/unmapped)
Fragments: 41310564 total (39870351 tlen-paired, 9850 hash-paired, 7277 singletons, 288570 discordant, 1134516 orphans, 112239 too large [>5000 bp], 9625705 duplicates)