Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/639bc4a596c514a864d7e0f071fbfe/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_B0O-N1-BDNA-1_A23FG3YLT4_1/869_B0O-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
  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/5f/639bc4a596c514a864d7e0f071fbfe/.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_B0O-N1-BDNA-1_A23FG3YLT4_1/869_B0O-N1-BDNA-1_A23FG3YLT4_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: 869_B0O-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_B0O-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.baiThe index file is older than the data file: 869_B0O-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_B0O-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: 71831867 total, 51276 skipped (flags/unmapped)
Fragments: 36014137 total (35742454 tlen-paired, 3851 hash-paired, 324 singletons, 10113 discordant, 257395 orphans, 5018 too large [>5000 bp], 9076622 duplicates)
Reads: 78493809 total, 44805 skipped (flags/unmapped)
Fragments: 39356803 total (39064695 tlen-paired, 2361 hash-paired, 400 singletons, 7035 discordant, 282312 orphans, 9055 too large [>5000 bp], 9730452 duplicates)
Reads: 80388660 total, 80492 skipped (flags/unmapped)
Fragments: 40425482 total (39593085 tlen-paired, 3785 hash-paired, 354 singletons, 158432 discordant, 669826 orphans, 63692 too large [>5000 bp], 10057680 duplicates)
Reads: 79514178 total, 49873 skipped (flags/unmapped)
Fragments: 39865531 total (39555389 tlen-paired, 5388 hash-paired, 349 singletons, 9581 discordant, 294824 orphans, 14208 too large [>5000 bp], 9937321 duplicates)