Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/e33d62673538a9e6420ca0073f8ab3/.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/ca/e33d62673538a9e6420ca0073f8ab3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_5O3-N1-BDNA-1_235YY7LT3_1/1029_5O3-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_5O3-N1-BDNA-1_235YY7LT3_1/1029_5O3-N1-BDNA-1_235YY7LT3_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_5O3-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5O3-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5O3-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5O3-N1-BDNA-1_235YY7LT3_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: 69427890 total, 59305 skipped (flags/unmapped)
Fragments: 34825484 total (34515771 tlen-paired, 5280 hash-paired, 4333 singletons, 11924 discordant, 288176 orphans, 5063 too large [>5000 bp], 7956530 duplicates)
Reads: 74821572 total, 52685 skipped (flags/unmapped)
Fragments: 37530079 total (37210639 tlen-paired, 4049 hash-paired, 4624 singletons, 8644 discordant, 302123 orphans, 7738 too large [>5000 bp], 8442709 duplicates)
Reads: 76548483 total, 57423 skipped (flags/unmapped)
Fragments: 38392300 total (38049428 tlen-paired, 4892 hash-paired, 4719 singletons, 11560 discordant, 321701 orphans, 16440 too large [>5000 bp], 8680852 duplicates)
Reads: 77375097 total, 84673 skipped (flags/unmapped)
Fragments: 38939544 total (38036302 tlen-paired, 4263 hash-paired, 4942 singletons, 168525 discordant, 725512 orphans, 70895 too large [>5000 bp], 8789058 duplicates)