Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1047_HD-N1-BDNA-1_A23TY32LT4_1/1047_HD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/0dda93109cd1a02c9f9db9865e8713/.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/46/0dda93109cd1a02c9f9db9865e8713/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1047_HD-N1-BDNA-1_A23TY32LT4_1/1047_HD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

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: 1047_HD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1047_HD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_HD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_HD-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: 108798660 total, 76859 skipped (flags/unmapped)
Fragments: 54528559 total (54153844 tlen-paired, 4422 hash-paired, 468 singletons, 15916 discordant, 353909 orphans, 9530 too large [>5000 bp], 22367311 duplicates)
Reads: 117360438 total, 65339 skipped (flags/unmapped)
Fragments: 58823414 total (58433979 tlen-paired, 3756 hash-paired, 545 singletons, 11292 discordant, 373842 orphans, 11329 too large [>5000 bp], 23881983 duplicates)
Reads: 129654883 total, 123086 skipped (flags/unmapped)
Fragments: 65127126 total (64011474 tlen-paired, 5212 hash-paired, 458 singletons, 215695 discordant, 894287 orphans, 86145 too large [>5000 bp], 26945452 duplicates)
Reads: 128275551 total, 71800 skipped (flags/unmapped)
Fragments: 64294994 total (63833070 tlen-paired, 6023 hash-paired, 395 singletons, 16274 discordant, 439232 orphans, 26695 too large [>5000 bp], 26568651 duplicates)