Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_IYU-N1-BDNA-1_A23TY32LT4_1/1029_IYU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/17ada09fecbca26841a3390d2c2e8e/.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/4e/17ada09fecbca26841a3390d2c2e8e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_IYU-N1-BDNA-1_A23TY32LT4_1/1029_IYU-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: 1029_IYU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYU-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: 54971146 total, 46753 skipped (flags/unmapped)
Fragments: 27619640 total (27279721 tlen-paired, 2735 hash-paired, 263 singletons, 7177 discordant, 329744 orphans, 7560 too large [>5000 bp], 10631463 duplicates)
Reads: 59500002 total, 42306 skipped (flags/unmapped)
Fragments: 29903942 total (29515277 tlen-paired, 2723 hash-paired, 242 singletons, 6298 discordant, 379402 orphans, 14728 too large [>5000 bp], 11533361 duplicates)
Reads: 59995861 total, 39364 skipped (flags/unmapped)
Fragments: 30156613 total (29778744 tlen-paired, 2287 hash-paired, 276 singletons, 5579 discordant, 369727 orphans, 6637 too large [>5000 bp], 11356735 duplicates)
Reads: 66375153 total, 78291 skipped (flags/unmapped)
Fragments: 33530687 total (32319725 tlen-paired, 2534 hash-paired, 258 singletons, 248734 discordant, 959436 orphans, 97591 too large [>5000 bp], 12796141 duplicates)