Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/c31f42b6f3e7e20f208d4d95d89715/.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/74/c31f42b6f3e7e20f208d4d95d89715/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/659_91-N1-BDNA-1_A23FG3YLT4_1/659_91-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/659_91-N1-BDNA-1_A23FG3YLT4_1/659_91-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: 659_91-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_91-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_91-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_91-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: 52658055 total, 38571 skipped (flags/unmapped)
Fragments: 26398367 total (26203583 tlen-paired, 2181 hash-paired, 273 singletons, 7849 discordant, 184481 orphans, 3752 too large [>5000 bp], 5817926 duplicates)
Reads: 57443327 total, 34803 skipped (flags/unmapped)
Fragments: 28797393 total (28589234 tlen-paired, 3280 hash-paired, 350 singletons, 5543 discordant, 198986 orphans, 6537 too large [>5000 bp], 6247311 duplicates)
Reads: 58014219 total, 38028 skipped (flags/unmapped)
Fragments: 29083975 total (28859072 tlen-paired, 3256 hash-paired, 342 singletons, 7788 discordant, 213517 orphans, 11050 too large [>5000 bp], 6345511 duplicates)
Reads: 58760333 total, 57711 skipped (flags/unmapped)
Fragments: 29542405 total (28960865 tlen-paired, 2067 hash-paired, 297 singletons, 109913 discordant, 469263 orphans, 43686 too large [>5000 bp], 6434220 duplicates)