Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_BD-N1-BDNA-1_A23TNVNLT4_1/1267_BD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/b70d4df93e6e35f57febb21ca6c4d8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_BD-N1-BDNA-1_A23TNVNLT4_1/1267_BD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  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/88/b70d4df93e6e35f57febb21ca6c4d8/.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: 1267_BD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BD-N1-BDNA-1_A23TNVNLT4_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: 89658011 total, 46104 skipped (flags/unmapped)
Fragments: 44919414 total (44662902 tlen-paired, 3041 hash-paired, 431 singletons, 9690 discordant, 243350 orphans, 8430 too large [>5000 bp], 15344165 duplicates)
Reads: 84205760 total, 58187 skipped (flags/unmapped)
Fragments: 42184216 total (41926990 tlen-paired, 5023 hash-paired, 392 singletons, 13622 discordant, 238189 orphans, 8861 too large [>5000 bp], 14623248 duplicates)
Reads: 99730131 total, 88827 skipped (flags/unmapped)
Fragments: 50042819 total (49356102 tlen-paired, 4970 hash-paired, 376 singletons, 129579 discordant, 551792 orphans, 53917 too large [>5000 bp], 17464968 duplicates)
Reads: 98184071 total, 52979 skipped (flags/unmapped)
Fragments: 49190688 total (48879643 tlen-paired, 6344 hash-paired, 381 singletons, 14005 discordant, 290315 orphans, 20206 too large [>5000 bp], 17150264 duplicates)