Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/55e7b36c65795ebe8692d7d99a4a48/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_DEX-N1-BDNA-1_A23TY7KLT4_1/1241_DEX-N1-BDNA-1_A23TY7KLT4_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/ba/55e7b36c65795ebe8692d7d99a4a48/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_DEX-N1-BDNA-1_A23TY7KLT4_1/1241_DEX-N1-BDNA-1_A23TY7KLT4_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: 1241_DEX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_DEX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_DEX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_DEX-N1-BDNA-1_A23TY7KLT4_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: 70263054 total, 52321 skipped (flags/unmapped)
Fragments: 35206305 total (34976987 tlen-paired, 3329 hash-paired, 324 singletons, 10130 discordant, 215535 orphans, 6991 too large [>5000 bp], 11620547 duplicates)
Reads: 75268835 total, 44651 skipped (flags/unmapped)
Fragments: 37719844 total (37479760 tlen-paired, 2717 hash-paired, 228 singletons, 8183 discordant, 228956 orphans, 6840 too large [>5000 bp], 12525002 duplicates)
Reads: 76309761 total, 43437 skipped (flags/unmapped)
Fragments: 38241038 total (38002658 tlen-paired, 1955 hash-paired, 361 singletons, 7289 discordant, 228775 orphans, 6692 too large [>5000 bp], 12353901 duplicates)
Reads: 82594864 total, 79409 skipped (flags/unmapped)
Fragments: 41470687 total (40808886 tlen-paired, 1980 hash-paired, 265 singletons, 129884 discordant, 529672 orphans, 52009 too large [>5000 bp], 13770665 duplicates)