Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/ad18b51b8c1c8596294a377a528742/.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/31/ad18b51b8c1c8596294a377a528742/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_HTR-N1-BDNA-1_A23NMNVLT4_1/1029_HTR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_HTR-N1-BDNA-1_A23NMNVLT4_1/1029_HTR-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] The index file is older than the data file: 1029_HTR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HTR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HTR-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HTR-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: 74491761 total, 47883 skipped (flags/unmapped)
Fragments: 37311700 total (37103169 tlen-paired, 2776 hash-paired, 356 singletons, 9879 discordant, 195520 orphans, 8177 too large [>5000 bp], 8564314 duplicates)
Reads: 79913307 total, 43136 skipped (flags/unmapped)
Fragments: 40027064 total (39817430 tlen-paired, 2589 hash-paired, 352 singletons, 6872 discordant, 199821 orphans, 8108 too large [>5000 bp], 9090788 duplicates)
Reads: 88333638 total, 72442 skipped (flags/unmapped)
Fragments: 44317282 total (43736300 tlen-paired, 2035 hash-paired, 381 singletons, 110235 discordant, 468331 orphans, 47672 too large [>5000 bp], 10400475 duplicates)
Reads: 87171300 total, 44461 skipped (flags/unmapped)
Fragments: 43667345 total (43400779 tlen-paired, 4692 hash-paired, 260 singletons, 10463 discordant, 251151 orphans, 21780 too large [>5000 bp], 10246903 duplicates)