Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/9782b837e3a7ee776bb1d0ab0ba192/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_H3F-N1-BDNA-1_B23L5TMLT4_1/1029_H3F-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  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/ab/9782b837e3a7ee776bb1d0ab0ba192/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_H3F-N1-BDNA-1_B23L5TMLT4_1/1029_H3F-N1-BDNA-1_B23L5TMLT4_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: 1029_H3F-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H3F-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1029_H3F-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_H3F-N1-BDNA-1_B23L5TMLT4_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: 92118059 total, 74872 skipped (flags/unmapped)
Fragments: 46249734 total (45742396 tlen-paired, 5667 hash-paired, 472 singletons, 17026 discordant, 484173 orphans, 14182 too large [>5000 bp], 18533964 duplicates)
Reads: 98336329 total, 59706 skipped (flags/unmapped)
Fragments: 49379990 total (48858190 tlen-paired, 3737 hash-paired, 620 singletons, 11576 discordant, 505867 orphans, 11565 too large [>5000 bp], 19502616 duplicates)
Reads: 107398782 total, 66900 skipped (flags/unmapped)
Fragments: 53930216 total (53336208 tlen-paired, 6025 hash-paired, 497 singletons, 16985 discordant, 570501 orphans, 21224 too large [>5000 bp], 21671064 duplicates)
Reads: 109339895 total, 112424 skipped (flags/unmapped)
Fragments: 55131221 total (53514849 tlen-paired, 3919 hash-paired, 523 singletons, 317126 discordant, 1294804 orphans, 130178 too large [>5000 bp], 22038127 duplicates)