Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_02P-N1-BDNA-1_A23NMNVLT4_1/1136_02P-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/699f00450775b72ff794b23c71f577/.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/cd/699f00450775b72ff794b23c71f577/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_02P-N1-BDNA-1_A23NMNVLT4_1/1136_02P-N1-BDNA-1_A23NMNVLT4_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: 1136_02P-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_02P-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_02P-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_02P-N1-BDNA-1_A23NMNVLT4_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: 66737321 total, 48063 skipped (flags/unmapped)
Fragments: 33436557 total (33227880 tlen-paired, 2242 hash-paired, 253 singletons, 9775 discordant, 196407 orphans, 6402 too large [>5000 bp], 9875914 duplicates)
Reads: 72466662 total, 40360 skipped (flags/unmapped)
Fragments: 36307805 total (36095881 tlen-paired, 1597 hash-paired, 273 singletons, 6875 discordant, 203179 orphans, 7072 too large [>5000 bp], 10532650 duplicates)
Reads: 72456808 total, 43870 skipped (flags/unmapped)
Fragments: 36309496 total (36057039 tlen-paired, 3720 hash-paired, 218 singletons, 8533 discordant, 239986 orphans, 17075 too large [>5000 bp], 10843619 duplicates)
Reads: 80071674 total, 78461 skipped (flags/unmapped)
Fragments: 40181344 total (39594664 tlen-paired, 3118 hash-paired, 332 singletons, 114739 discordant, 468491 orphans, 49674 too large [>5000 bp], 12023386 duplicates)