Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BN1U-N1-BDNA-1_A23KFG7LT4_1/1029_BN1U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BN1U-N1-BDNA-1_A23KFG7LT4_1/1029_BN1U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/cf7379812e3963e005c092cfa64c4b/.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/69/cf7379812e3963e005c092cfa64c4b/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BN1U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BN1U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BN1U-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BN1U-N1-BDNA-1_A23KFG7LT4_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: 82661839 total, 57121 skipped (flags/unmapped)
Fragments: 41529671 total (41037147 tlen-paired, 2890 hash-paired, 507 singletons, 14482 discordant, 474645 orphans, 10264 too large [>5000 bp], 14910936 duplicates)
Reads: 88608333 total, 50072 skipped (flags/unmapped)
Fragments: 44518915 total (44007124 tlen-paired, 2297 hash-paired, 495 singletons, 10333 discordant, 498666 orphans, 9796 too large [>5000 bp], 15590445 duplicates)
Reads: 96765780 total, 54093 skipped (flags/unmapped)
Fragments: 48619484 total (48026117 tlen-paired, 3496 hash-paired, 411 singletons, 15388 discordant, 574072 orphans, 23601 too large [>5000 bp], 17510722 duplicates)
Reads: 98427940 total, 87752 skipped (flags/unmapped)
Fragments: 49689226 total (48065033 tlen-paired, 2391 hash-paired, 500 singletons, 321002 discordant, 1300300 orphans, 131268 too large [>5000 bp], 17819052 duplicates)