Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_G7Y-N1-BDNA-1_A23FG3YLT4_1/869_G7Y-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/8c0906b7e120e3151a4cb155fb2b8a/.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/8e/8c0906b7e120e3151a4cb155fb2b8a/.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_G7Y-N1-BDNA-1_A23FG3YLT4_1/869_G7Y-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_G7Y-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G7Y-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G7Y-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G7Y-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: 67217945 total, 45538 skipped (flags/unmapped)
Fragments: 33679516 total (33469943 tlen-paired, 3397 hash-paired, 363 singletons, 9711 discordant, 196102 orphans, 4920 too large [>5000 bp], 7385001 duplicates)
Reads: 73853019 total, 41999 skipped (flags/unmapped)
Fragments: 37002409 total (36780073 tlen-paired, 4087 hash-paired, 404 singletons, 7207 discordant, 210638 orphans, 8622 too large [>5000 bp], 8002599 duplicates)
Reads: 74662378 total, 67832 skipped (flags/unmapped)
Fragments: 37486084 total (36914749 tlen-paired, 2599 hash-paired, 347 singletons, 105392 discordant, 462997 orphans, 42861 too large [>5000 bp], 8184301 duplicates)
Reads: 74115017 total, 46094 skipped (flags/unmapped)
Fragments: 37132606 total (36891398 tlen-paired, 5068 hash-paired, 324 singletons, 9507 discordant, 226309 orphans, 15172 too large [>5000 bp], 8074689 duplicates)