Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_DK8-N1-BDNA-1_B23KFG5LT4_1/1029_DK8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/04769ea82170cfa3ccc80b5ff2bd06/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_DK8-N1-BDNA-1_B23KFG5LT4_1/1029_DK8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  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/8e/04769ea82170cfa3ccc80b5ff2bd06/.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: 1029_DK8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DK8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DK8-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DK8-N1-BDNA-1_B23KFG5LT4_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: 70430720 total, 46552 skipped (flags/unmapped)
Fragments: 35275811 total (35044662 tlen-paired, 4495 hash-paired, 266 singletons, 9198 discordant, 217190 orphans, 25001 too large [>5000 bp], 13288214 duplicates)
Reads: 70529317 total, 41161 skipped (flags/unmapped)
Fragments: 35327038 total (35134240 tlen-paired, 2531 hash-paired, 318 singletons, 7163 discordant, 182786 orphans, 8592 too large [>5000 bp], 13011867 duplicates)
Reads: 66214103 total, 51571 skipped (flags/unmapped)
Fragments: 33156861 total (32971499 tlen-paired, 3275 hash-paired, 351 singletons, 10495 discordant, 171241 orphans, 10201 too large [>5000 bp], 12535534 duplicates)
Reads: 77450745 total, 76433 skipped (flags/unmapped)
Fragments: 38842838 total (38361105 tlen-paired, 3685 hash-paired, 347 singletons, 91560 discordant, 386141 orphans, 37562 too large [>5000 bp], 14674351 duplicates)