Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_G9Q-N1-BDNA-1_B23KFG5LT4_1/1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/7304189b4b5ba22027b44e5a081f05/.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/b7/7304189b4b5ba22027b44e5a081f05/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_G9Q-N1-BDNA-1_B23KFG5LT4_1/1029_G9Q-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] The index file is older than the data file: 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_G9Q-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_G9Q-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: 70274807 total, 54850 skipped (flags/unmapped)
Fragments: 35216989 total (34964006 tlen-paired, 3999 hash-paired, 334 singletons, 12721 discordant, 235929 orphans, 11121 too large [>5000 bp], 13722354 duplicates)
Reads: 75307974 total, 44477 skipped (flags/unmapped)
Fragments: 37745481 total (37487541 tlen-paired, 2166 hash-paired, 346 singletons, 9235 discordant, 246193 orphans, 9537 too large [>5000 bp], 14390375 duplicates)
Reads: 82706348 total, 50151 skipped (flags/unmapped)
Fragments: 41456599 total (41152764 tlen-paired, 5266 hash-paired, 321 singletons, 12800 discordant, 285448 orphans, 14384 too large [>5000 bp], 16185129 duplicates)
Reads: 83066444 total, 79193 skipped (flags/unmapped)
Fragments: 41719537 total (41028916 tlen-paired, 1514 hash-paired, 331 singletons, 131108 discordant, 557668 orphans, 53088 too large [>5000 bp], 16322053 duplicates)