Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_XTN-N1-BDNA-1_A23FG3YLT4_1/869_XTN-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/2d92fed81622fa0fdee4bb4a106882/.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_XTN-N1-BDNA-1_A23FG3YLT4_1/869_XTN-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  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/73/2d92fed81622fa0fdee4bb4a106882/.command.run
==> 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_XTN-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_XTN-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XTN-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XTN-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: 58466294 total, 39854 skipped (flags/unmapped)
Fragments: 29300932 total (29105041 tlen-paired, 3438 hash-paired, 257 singletons, 8907 discordant, 183289 orphans, 4061 too large [>5000 bp], 6673135 duplicates)
Reads: 58765187 total, 37822 skipped (flags/unmapped)
Fragments: 29450660 total (29241307 tlen-paired, 3230 hash-paired, 262 singletons, 7370 discordant, 198491 orphans, 12399 too large [>5000 bp], 6648459 duplicates)
Reads: 64636668 total, 34728 skipped (flags/unmapped)
Fragments: 32394563 total (32183628 tlen-paired, 3093 hash-paired, 365 singletons, 6172 discordant, 201305 orphans, 7242 too large [>5000 bp], 7238500 duplicates)
Reads: 65170159 total, 56067 skipped (flags/unmapped)
Fragments: 32735928 total (32186981 tlen-paired, 2014 hash-paired, 281 singletons, 105347 discordant, 441305 orphans, 41911 too large [>5000 bp], 7408509 duplicates)