Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2RO-N1-BDNA-1_A23H3NYLT3_1/1136_2RO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/102ad353b10394544040f0066e8a2b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2RO-N1-BDNA-1_A23H3NYLT3_1/1136_2RO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  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/a8/102ad353b10394544040f0066e8a2b/.command.run
==> 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_2RO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_2RO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2RO-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2RO-N1-BDNA-1_A23H3NYLT3_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: 82234016 total, 69282 skipped (flags/unmapped)
Fragments: 41356954 total (40761598 tlen-paired, 14250 hash-paired, 9026 singletons, 8688 discordant, 563392 orphans, 11622 too large [>5000 bp], 6369759 duplicates)
Reads: 83123997 total, 78058 skipped (flags/unmapped)
Fragments: 41787837 total (41212405 tlen-paired, 13071 hash-paired, 9326 singletons, 9394 discordant, 543641 orphans, 11616 too large [>5000 bp], 6486521 duplicates)
Reads: 91407336 total, 69788 skipped (flags/unmapped)
Fragments: 45978006 total (45313501 tlen-paired, 12997 hash-paired, 9908 singletons, 7896 discordant, 633704 orphans, 12574 too large [>5000 bp], 7029956 duplicates)
Reads: 92653648 total, 116126 skipped (flags/unmapped)
Fragments: 46914386 total (44906682 tlen-paired, 12855 hash-paired, 10117 singletons, 404397 discordant, 1580335 orphans, 149601 too large [>5000 bp], 7087951 duplicates)