Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_3Q4-N1-BDNA-1_B23KFG5LT4_1/1136_3Q4-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/c798d162c525949c29c81b039f5606/.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/7d/c798d162c525949c29c81b039f5606/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_3Q4-N1-BDNA-1_B23KFG5LT4_1/1136_3Q4-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: 1136_3Q4-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3Q4-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3Q4-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3Q4-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: 97812441 total, 68357 skipped (flags/unmapped)
Fragments: 49051714 total (48610869 tlen-paired, 7035 hash-paired, 392 singletons, 17608 discordant, 415810 orphans, 28429 too large [>5000 bp], 21227282 duplicates)
Reads: 91787072 total, 72486 skipped (flags/unmapped)
Fragments: 46023547 total (45633604 tlen-paired, 3303 hash-paired, 468 singletons, 20134 discordant, 366038 orphans, 16999 too large [>5000 bp], 19924131 duplicates)
Reads: 97361009 total, 61507 skipped (flags/unmapped)
Fragments: 48827464 total (48431175 tlen-paired, 2609 hash-paired, 508 singletons, 14286 discordant, 378886 orphans, 11984 too large [>5000 bp], 20621243 duplicates)
Reads: 108057449 total, 102906 skipped (flags/unmapped)
Fragments: 54314799 total (53264876 tlen-paired, 4264 hash-paired, 430 singletons, 204320 discordant, 840909 orphans, 83142 too large [>5000 bp], 23536326 duplicates)