Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_QEF-N1-BDNA-1_A23KFG7LT4_1/1029_QEF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/bf16730fc22cf11b0932d07578450e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/bf16730fc22cf11b0932d07578450e/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_QEF-N1-BDNA-1_A23KFG7LT4_1/1029_QEF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> 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_QEF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_QEF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_QEF-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_QEF-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: 59867165 total, 39022 skipped (flags/unmapped)
Fragments: 29998457 total (29807045 tlen-paired, 1737 hash-paired, 252 singletons, 6774 discordant, 182649 orphans, 7065 too large [>5000 bp], 9591642 duplicates)
Reads: 64710497 total, 34508 skipped (flags/unmapped)
Fragments: 32428498 total (32225012 tlen-paired, 2971 hash-paired, 340 singletons, 4658 discordant, 195517 orphans, 7425 too large [>5000 bp], 10050330 duplicates)
Reads: 63637550 total, 35942 skipped (flags/unmapped)
Fragments: 31896594 total (31671302 tlen-paired, 3677 hash-paired, 275 singletons, 5909 discordant, 215431 orphans, 12063 too large [>5000 bp], 10198970 duplicates)
Reads: 70403332 total, 59858 skipped (flags/unmapped)
Fragments: 35361001 total (34763790 tlen-paired, 1811 hash-paired, 292 singletons, 119158 discordant, 475950 orphans, 48857 too large [>5000 bp], 11300466 duplicates)