Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_e6H-N1-BDNA-1_A23TY32LT4_1/659_e6H-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/f1afad01ad6f4753fbc89bb5fceb05/.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/77/f1afad01ad6f4753fbc89bb5fceb05/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_e6H-N1-BDNA-1_A23TY32LT4_1/659_e6H-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_e6H-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_e6H-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_e6H-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_e6H-N1-BDNA-1_A23TY32LT4_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: 104289916 total, 74370 skipped (flags/unmapped)
Fragments: 52280620 total (51888112 tlen-paired, 5021 hash-paired, 445 singletons, 15821 discordant, 371221 orphans, 12986 too large [>5000 bp], 20398769 duplicates)
Reads: 113570633 total, 64779 skipped (flags/unmapped)
Fragments: 56937103 total (56526923 tlen-paired, 5842 hash-paired, 527 singletons, 10984 discordant, 392827 orphans, 12501 too large [>5000 bp], 21946695 duplicates)
Reads: 113355277 total, 66419 skipped (flags/unmapped)
Fragments: 56834041 total (56396127 tlen-paired, 6807 hash-paired, 359 singletons, 13031 discordant, 417717 orphans, 19426 too large [>5000 bp], 22416756 duplicates)
Reads: 124873552 total, 112999 skipped (flags/unmapped)
Fragments: 62754892 total (61580333 tlen-paired, 5465 hash-paired, 442 singletons, 233691 discordant, 934961 orphans, 93086 too large [>5000 bp], 24701372 duplicates)