Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BSJ5-N1-BDNA-1_A23TY32LT4_1/1241_BSJ5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/0af6bcdb014354c410217d0b61cb4c/.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/3b/0af6bcdb014354c410217d0b61cb4c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_BSJ5-N1-BDNA-1_A23TY32LT4_1/1241_BSJ5-N1-BDNA-1_A23TY32LT4_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_BSJ5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BSJ5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BSJ5-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BSJ5-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: 93250634 total, 67501 skipped (flags/unmapped)
Fragments: 46725051 total (46418678 tlen-paired, 5384 hash-paired, 404 singletons, 12584 discordant, 288001 orphans, 10718 too large [>5000 bp], 17911550 duplicates)
Reads: 101018295 total, 55386 skipped (flags/unmapped)
Fragments: 50623766 total (50305198 tlen-paired, 2919 hash-paired, 555 singletons, 8682 discordant, 306412 orphans, 11172 too large [>5000 bp], 19122717 duplicates)
Reads: 109898427 total, 61160 skipped (flags/unmapped)
Fragments: 55081521 total (54699236 tlen-paired, 4224 hash-paired, 322 singletons, 12700 discordant, 365039 orphans, 19793 too large [>5000 bp], 21225988 duplicates)
Reads: 111344371 total, 110163 skipped (flags/unmapped)
Fragments: 55913913 total (54987172 tlen-paired, 4694 hash-paired, 369 singletons, 179677 discordant, 742001 orphans, 74376 too large [>5000 bp], 21553758 duplicates)