Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/d06203ec5b9e565f32d4bed28c0541/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_NGX-N1-BDNA-1_A23FG3YLT4_1/869_NGX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/d06203ec5b9e565f32d4bed28c0541/.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_NGX-N1-BDNA-1_A23FG3YLT4_1/869_NGX-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_NGX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_NGX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_NGX-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_NGX-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: 69174445 total, 44473 skipped (flags/unmapped)
Fragments: 34650925 total (34442202 tlen-paired, 3222 hash-paired, 349 singletons, 7673 discordant, 197479 orphans, 12975 too large [>5000 bp], 7735010 duplicates)
Reads: 68660327 total, 44737 skipped (flags/unmapped)
Fragments: 34392933 total (34201443 tlen-paired, 3006 hash-paired, 312 singletons, 8854 discordant, 179318 orphans, 4677 too large [>5000 bp], 7773667 duplicates)
Reads: 75907515 total, 41511 skipped (flags/unmapped)
Fragments: 38024646 total (37816294 tlen-paired, 3361 hash-paired, 406 singletons, 6907 discordant, 197678 orphans, 7398 too large [>5000 bp], 8420446 duplicates)
Reads: 76340477 total, 66964 skipped (flags/unmapped)
Fragments: 38307119 total (37784071 tlen-paired, 1885 hash-paired, 358 singletons, 98598 discordant, 422207 orphans, 40920 too large [>5000 bp], 8581465 duplicates)