Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_8BN-N1-BDNA-1_A23NLN3LT4_1/1136_8BN-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_8BN-N1-BDNA-1_A23NLN3LT4_1/1136_8BN-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/cc9f332fbc590c1d6c2d9e97317e28/.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/81/cc9f332fbc590c1d6c2d9e97317e28/.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: 1136_8BN-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_8BN-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8BN-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8BN-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: 92477723 total, 68134 skipped (flags/unmapped)
Fragments: 46367600 total (45992763 tlen-paired, 4490 hash-paired, 459 singletons, 17424 discordant, 352464 orphans, 13656 too large [>5000 bp], 16706126 duplicates)
Reads: 99906785 total, 56305 skipped (flags/unmapped)
Fragments: 50094518 total (49714521 tlen-paired, 3654 hash-paired, 497 singletons, 12117 discordant, 363729 orphans, 12835 too large [>5000 bp], 17731667 duplicates)
Reads: 108762309 total, 61849 skipped (flags/unmapped)
Fragments: 54540082 total (54079410 tlen-paired, 3900 hash-paired, 447 singletons, 18124 discordant, 438201 orphans, 29472 too large [>5000 bp], 19784913 duplicates)
Reads: 109722067 total, 101827 skipped (flags/unmapped)
Fragments: 55151059 total (54087762 tlen-paired, 5439 hash-paired, 411 singletons, 203452 discordant, 853995 orphans, 86264 too large [>5000 bp], 20023289 duplicates)