Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_KAF-N1-BDNA-1_A237CFYLT3_1/869_KAF-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_KAF-N1-BDNA-1_A237CFYLT3_1/869_KAF-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/ed78b0f4eb615d1aeb337a30caedde/.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/a5/ed78b0f4eb615d1aeb337a30caedde/.command.run
==> 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_KAF-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_KAF-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_KAF-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_KAF-N1-BDNA-1_A237CFYLT3_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: 67250058 total, 72278 skipped (flags/unmapped)
Fragments: 33864514 total (33289906 tlen-paired, 5316 hash-paired, 8458 singletons, 9336 discordant, 551498 orphans, 4354 too large [>5000 bp], 6447330 duplicates)
Reads: 73385007 total, 69962 skipped (flags/unmapped)
Fragments: 36959461 total (36324579 tlen-paired, 5394 hash-paired, 9025 singletons, 6499 discordant, 613964 orphans, 9556 too large [>5000 bp], 7038041 duplicates)
Reads: 74773415 total, 69882 skipped (flags/unmapped)
Fragments: 37656554 total (36997092 tlen-paired, 6806 hash-paired, 9259 singletons, 9657 discordant, 633740 orphans, 16712 too large [>5000 bp], 7125109 duplicates)
Reads: 77642621 total, 167292 skipped (flags/unmapped)
Fragments: 39404035 total (37334516 tlen-paired, 6212 hash-paired, 9657 singletons, 406388 discordant, 1647262 orphans, 162089 too large [>5000 bp], 7350675 duplicates)