Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/ddcc12feea5378031b2c3e9082e599/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_IB1-N1-BDNA-1_A23NLN3LT4_1/1029_IB1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  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/4f/ddcc12feea5378031b2c3e9082e599/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_IB1-N1-BDNA-1_A23NLN3LT4_1/1029_IB1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> 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_IB1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_IB1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_IB1-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IB1-N1-BDNA-1_A23NLN3LT4_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: 66825344 total, 54999 skipped (flags/unmapped)
Fragments: 33501916 total (33232805 tlen-paired, 2730 hash-paired, 343 singletons, 14830 discordant, 251208 orphans, 9032 too large [>5000 bp], 11246284 duplicates)
Reads: 71923595 total, 46041 skipped (flags/unmapped)
Fragments: 36058980 total (35785756 tlen-paired, 3010 hash-paired, 270 singletons, 10108 discordant, 259836 orphans, 9850 too large [>5000 bp], 11916854 duplicates)
Reads: 79175787 total, 80526 skipped (flags/unmapped)
Fragments: 39778104 total (39068938 tlen-paired, 2155 hash-paired, 301 singletons, 134606 discordant, 572104 orphans, 55729 too large [>5000 bp], 13452943 duplicates)
Reads: 78350075 total, 49705 skipped (flags/unmapped)
Fragments: 39281441 total (38959250 tlen-paired, 3135 hash-paired, 292 singletons, 15320 discordant, 303444 orphans, 20612 too large [>5000 bp], 13278389 duplicates)