Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_DOI-N1-BDNA-1_A23H3NYLT3_1/869_DOI-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/ecb362162eb89a88335633bbec3212/.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/2f/ecb362162eb89a88335633bbec3212/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_DOI-N1-BDNA-1_A23H3NYLT3_1/869_DOI-N1-BDNA-1_A23H3NYLT3_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: 869_DOI-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DOI-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DOI-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DOI-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: 88932229 total, 71411 skipped (flags/unmapped)
Fragments: 44602396 total (44205136 tlen-paired, 25386 hash-paired, 9695 singletons, 8250 discordant, 353929 orphans, 9825 too large [>5000 bp], 6318583 duplicates)
Reads: 95842960 total, 69147 skipped (flags/unmapped)
Fragments: 48076772 total (47627370 tlen-paired, 26519 hash-paired, 10185 singletons, 8732 discordant, 403966 orphans, 17210 too large [>5000 bp], 6755807 duplicates)
Reads: 96121314 total, 64629 skipped (flags/unmapped)
Fragments: 48224529 total (47777734 tlen-paired, 26277 hash-paired, 10134 singletons, 6865 discordant, 403519 orphans, 10640 too large [>5000 bp], 6767316 duplicates)
Reads: 97555425 total, 115042 skipped (flags/unmapped)
Fragments: 49132996 total (47844019 tlen-paired, 27184 hash-paired, 10234 singletons, 244284 discordant, 1007275 orphans, 95950 too large [>5000 bp], 6853197 duplicates)