Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_bTo-N1-BDNA-1_B23KFG5LT4_1/659_bTo-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/ee8efbfc47b91fedf14bc41b32b8ce/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_bTo-N1-BDNA-1_B23KFG5LT4_1/659_bTo-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/6e/ee8efbfc47b91fedf14bc41b32b8ce/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-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: 70396641 total, 58468 skipped (flags/unmapped)
Fragments: 35311180 total (34983741 tlen-paired, 3862 hash-paired, 324 singletons, 14894 discordant, 308359 orphans, 12248 too large [>5000 bp], 14428018 duplicates)
Reads: 73872064 total, 47582 skipped (flags/unmapped)
Fragments: 37059143 total (36734559 tlen-paired, 2325 hash-paired, 335 singletons, 9761 discordant, 312163 orphans, 9347 too large [>5000 bp], 14814570 duplicates)
Reads: 83262414 total, 82410 skipped (flags/unmapped)
Fragments: 41889922 total (40959004 tlen-paired, 3420 hash-paired, 330 singletons, 177746 discordant, 749422 orphans, 74956 too large [>5000 bp], 17160984 duplicates)
Reads: 82408200 total, 52884 skipped (flags/unmapped)
Fragments: 41346146 total (40943025 tlen-paired, 3080 hash-paired, 326 singletons, 15843 discordant, 383872 orphans, 23611 too large [>5000 bp], 16949598 duplicates)