Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_CN-N1-BDNA-1_A23TY32LT4_1/1241_CN-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/0f524e4bbd92967929f5a10ed6f0eb/.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/8f/0f524e4bbd92967929f5a10ed6f0eb/.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_CN-N1-BDNA-1_A23TY32LT4_1/1241_CN-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_CN-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CN-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CN-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_CN-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: 77094995 total, 58581 skipped (flags/unmapped)
Fragments: 38669463 total (38332995 tlen-paired, 3506 hash-paired, 347 singletons, 11226 discordant, 321389 orphans, 9612 too large [>5000 bp], 16108189 duplicates)
Reads: 82220631 total, 51149 skipped (flags/unmapped)
Fragments: 41247330 total (40891248 tlen-paired, 3019 hash-paired, 394 singletons, 7623 discordant, 345046 orphans, 10131 too large [>5000 bp], 16934640 duplicates)
Reads: 91092009 total, 52938 skipped (flags/unmapped)
Fragments: 45697647 total (45284283 tlen-paired, 5064 hash-paired, 275 singletons, 11497 discordant, 396528 orphans, 20290 too large [>5000 bp], 19111483 duplicates)
Reads: 92352900 total, 99481 skipped (flags/unmapped)
Fragments: 46477859 total (45385263 tlen-paired, 3469 hash-paired, 351 singletons, 216882 discordant, 871894 orphans, 84973 too large [>5000 bp], 19318446 duplicates)