Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_68-N1-BDNA-1_A23TY32LT4_1/1241_68-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/c229fedbd29b9e46df5c84a39387dd/.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/c3/c229fedbd29b9e46df5c84a39387dd/.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_68-N1-BDNA-1_A23TY32LT4_1/1241_68-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_68-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_68-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_68-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_68-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: 72635411 total, 55395 skipped (flags/unmapped)
Fragments: 36443458 total (36101411 tlen-paired, 4025 hash-paired, 330 singletons, 9838 discordant, 327854 orphans, 10642 too large [>5000 bp], 14543000 duplicates)
Reads: 78695149 total, 45896 skipped (flags/unmapped)
Fragments: 39498301 total (39124787 tlen-paired, 3105 hash-paired, 398 singletons, 6708 discordant, 363303 orphans, 8176 too large [>5000 bp], 15572777 duplicates)
Reads: 87408406 total, 96491 skipped (flags/unmapped)
Fragments: 44029128 total (42864001 tlen-paired, 3670 hash-paired, 374 singletons, 233304 discordant, 927779 orphans, 90906 too large [>5000 bp], 17559115 duplicates)
Reads: 86280337 total, 51023 skipped (flags/unmapped)
Fragments: 43304388 total (42863972 tlen-paired, 6065 hash-paired, 316 singletons, 10979 discordant, 423056 orphans, 21955 too large [>5000 bp], 17358107 duplicates)