Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_wS-N1-BDNA-1_A23TY32LT4_1/659_wS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/f6545cae9dbad4cb4a238dd21e6dab/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_wS-N1-BDNA-1_A23TY32LT4_1/659_wS-N1-BDNA-1_A23TY32LT4_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/a7/f6545cae9dbad4cb4a238dd21e6dab/.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: 659_wS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_wS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_wS-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_wS-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: 94490860 total, 55743 skipped (flags/unmapped)
Fragments: 47365866 total (47011592 tlen-paired, 7824 hash-paired, 289 singletons, 13587 discordant, 332574 orphans, 18124 too large [>5000 bp], 18391116 duplicates)
Reads: 87352318 total, 64526 skipped (flags/unmapped)
Fragments: 43780294 total (43462048 tlen-paired, 5434 hash-paired, 435 singletons, 15602 discordant, 296775 orphans, 12207 too large [>5000 bp], 16861692 duplicates)
Reads: 96310740 total, 52519 skipped (flags/unmapped)
Fragments: 48274176 total (47946909 tlen-paired, 3868 hash-paired, 465 singletons, 11148 discordant, 311786 orphans, 11060 too large [>5000 bp], 18353527 duplicates)
Reads: 104803047 total, 98962 skipped (flags/unmapped)
Fragments: 52630883 total (51753380 tlen-paired, 5164 hash-paired, 324 singletons, 172502 discordant, 699513 orphans, 71078 too large [>5000 bp], 20434113 duplicates)