Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BC0-N1-BDNA-1_B23KFG5LT4_1/1029_BC0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/86ce16182df180ce073a2b50feaf69/.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/cc/86ce16182df180ce073a2b50feaf69/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BC0-N1-BDNA-1_B23KFG5LT4_1/1029_BC0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BC0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BC0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BC0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BC0-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: 69805957 total, 56797 skipped (flags/unmapped)
Fragments: 35009386 total (34701974 tlen-paired, 3430 hash-paired, 367 singletons, 13864 discordant, 289751 orphans, 10253 too large [>5000 bp], 14706461 duplicates)
Reads: 75003497 total, 45729 skipped (flags/unmapped)
Fragments: 37623644 total (37302905 tlen-paired, 2448 hash-paired, 356 singletons, 9707 discordant, 308228 orphans, 9532 too large [>5000 bp], 15406016 duplicates)
Reads: 83717254 total, 50046 skipped (flags/unmapped)
Fragments: 41994412 total (41612581 tlen-paired, 3821 hash-paired, 285 singletons, 14404 discordant, 363321 orphans, 20995 too large [>5000 bp], 17702401 duplicates)
Reads: 84804913 total, 84294 skipped (flags/unmapped)
Fragments: 42656241 total (41739562 tlen-paired, 3389 hash-paired, 350 singletons, 179031 discordant, 733909 orphans, 71198 too large [>5000 bp], 17985691 duplicates)