Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/6f89b170946fa3090f698c867d2a6b/.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/80/6f89b170946fa3090f698c867d2a6b/.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_GL8-N1-BDNA-1_A23FG3YLT4_1/869_GL8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_GL8-N1-BDNA-1_A23FG3YLT4_1/869_GL8-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_GL8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_GL8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
The index file is older than the data file: 869_GL8-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_GL8-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 58592159 total, 42093 skipped (flags/unmapped)
Fragments: 29368325 total (29161318 tlen-paired, 2835 hash-paired, 332 singletons, 8898 discordant, 194942 orphans, 4345 too large [>5000 bp], 6535714 duplicates)
Reads: 64186235 total, 36838 skipped (flags/unmapped)
Fragments: 32171736 total (31953959 tlen-paired, 2329 hash-paired, 394 singletons, 6357 discordant, 208697 orphans, 7508 too large [>5000 bp], 7057172 duplicates)
Reads: 65490127 total, 63329 skipped (flags/unmapped)
Fragments: 32904424 total (32319671 tlen-paired, 2458 hash-paired, 293 singletons, 109573 discordant, 472429 orphans, 45336 too large [>5000 bp], 7253659 duplicates)
Reads: 64795943 total, 42235 skipped (flags/unmapped)
Fragments: 32473652 total (32240245 tlen-paired, 4132 hash-paired, 308 singletons, 8531 discordant, 220436 orphans, 13574 too large [>5000 bp], 7159614 duplicates)