Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BXGB-N1-BDNA-1_A23TY32LT4_1/1241_BXGB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/99e1c1b116f3e030e0cb4d34c16699/.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/85/99e1c1b116f3e030e0cb4d34c16699/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BXGB-N1-BDNA-1_A23TY32LT4_1/1241_BXGB-N1-BDNA-1_A23TY32LT4_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: 1241_BXGB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BXGB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_BXGB-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BXGB-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: 78390988 total, 65225 skipped (flags/unmapped)
Fragments: 39411518 total (38874061 tlen-paired, 3686 hash-paired, 381 singletons, 12970 discordant, 520420 orphans, 11764 too large [>5000 bp], 16830556 duplicates)
Reads: 84513432 total, 56487 skipped (flags/unmapped)
Fragments: 42505102 total (41917894 tlen-paired, 3566 hash-paired, 434 singletons, 8959 discordant, 574249 orphans, 10712 too large [>5000 bp], 17808131 duplicates)
Reads: 93302891 total, 61172 skipped (flags/unmapped)
Fragments: 46915995 total (46275265 tlen-paired, 3551 hash-paired, 316 singletons, 12652 discordant, 624211 orphans, 17128 too large [>5000 bp], 20115395 duplicates)
Reads: 95119901 total, 110415 skipped (flags/unmapped)
Fragments: 48115674 total (46200085 tlen-paired, 2785 hash-paired, 435 singletons, 387172 discordant, 1525197 orphans, 151885 too large [>5000 bp], 20370784 duplicates)