Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_B0C-N1-BDNA-1_A23FG3YLT4_1/869_B0C-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/0c36bd52b2818d86214213f984aafa/.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/75/0c36bd52b2818d86214213f984aafa/.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_B0C-N1-BDNA-1_A23FG3YLT4_1/869_B0C-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
==> 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: 869_B0C-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_B0C-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_B0C-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_B0C-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: 60988399 total, 40187 skipped (flags/unmapped)
Fragments: 30564681 total (30351094 tlen-paired, 3219 hash-paired, 339 singletons, 7438 discordant, 202591 orphans, 10890 too large [>5000 bp], 6684013 duplicates)
Reads: 67081273 total, 36070 skipped (flags/unmapped)
Fragments: 33620574 total (33399303 tlen-paired, 2891 hash-paired, 403 singletons, 6807 discordant, 211170 orphans, 7814 too large [>5000 bp], 7285262 duplicates)
Reads: 60813730 total, 40590 skipped (flags/unmapped)
Fragments: 30480073 total (30273535 tlen-paired, 2317 hash-paired, 352 singletons, 9099 discordant, 194770 orphans, 4058 too large [>5000 bp], 6743375 duplicates)
Reads: 67760844 total, 62495 skipped (flags/unmapped)
Fragments: 34036036 total (33456284 tlen-paired, 1403 hash-paired, 302 singletons, 111576 discordant, 466471 orphans, 46525 too large [>5000 bp], 7467370 duplicates)