Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/00e2eebcb8feb910bf274e7f099ca3/.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/b5/00e2eebcb8feb910bf274e7f099ca3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_XR8-N1-BDNA-1_A23FG3YLT4_1/869_XR8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_XR8-N1-BDNA-1_A23FG3YLT4_1/869_XR8-N1-BDNA-1_A23FG3YLT4_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_XR8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XR8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XR8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XR8-N1-BDNA-1_A23FG3YLT4_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: 50433977 total, 35921 skipped (flags/unmapped)
Fragments: 25288440 total (25089415 tlen-paired, 1967 hash-paired, 188 singletons, 10342 discordant, 186528 orphans, 3946 too large [>5000 bp], 5643990 duplicates)
Reads: 55451434 total, 31922 skipped (flags/unmapped)
Fragments: 27801574 total (27593723 tlen-paired, 2874 hash-paired, 300 singletons, 7195 discordant, 197482 orphans, 7073 too large [>5000 bp], 6138313 duplicates)
Reads: 55653475 total, 35957 skipped (flags/unmapped)
Fragments: 27900344 total (27679105 tlen-paired, 3315 hash-paired, 267 singletons, 9632 discordant, 208025 orphans, 12561 too large [>5000 bp], 6189449 duplicates)
Reads: 56388485 total, 52133 skipped (flags/unmapped)
Fragments: 28345869 total (27812505 tlen-paired, 1500 hash-paired, 294 singletons, 98604 discordant, 432966 orphans, 38937 too large [>5000 bp], 6272874 duplicates)