Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_K8V-N1-BDNA-1_A23H3NYLT3_1/869_K8V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/bd4a2c918148e03df895f34870ed96/.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/c0/bd4a2c918148e03df895f34870ed96/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_K8V-N1-BDNA-1_A23H3NYLT3_1/869_K8V-N1-BDNA-1_A23H3NYLT3_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: 869_K8V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K8V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K8V-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K8V-N1-BDNA-1_A23H3NYLT3_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: 76076697 total, 65455 skipped (flags/unmapped)
Fragments: 38225526 total (37747215 tlen-paired, 11596 hash-paired, 6992 singletons, 6501 discordant, 453222 orphans, 10202 too large [>5000 bp], 5134753 duplicates)
Reads: 82141053 total, 58525 skipped (flags/unmapped)
Fragments: 41288495 total (40757551 tlen-paired, 11510 hash-paired, 7277 singletons, 6280 discordant, 505877 orphans, 9346 too large [>5000 bp], 5500249 duplicates)
Reads: 82444086 total, 55826 skipped (flags/unmapped)
Fragments: 41454341 total (40896149 tlen-paired, 12253 hash-paired, 7353 singletons, 5427 discordant, 533159 orphans, 10045 too large [>5000 bp], 5504951 duplicates)
Reads: 83638100 total, 94330 skipped (flags/unmapped)
Fragments: 42341339 total (40599804 tlen-paired, 9566 hash-paired, 7467 singletons, 341909 discordant, 1382593 orphans, 125576 too large [>5000 bp], 5541840 duplicates)