Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_FGH-N1-BDNA-1_B2377KTLT3_3/869_FGH-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_FGH-N1-BDNA-1_B2377KTLT3_3/869_FGH-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/60b0e3056145d820c27d8ffdc6af7f/.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/67/60b0e3056145d820c27d8ffdc6af7f/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_FGH-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_FGH-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_FGH-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_FGH-N1-BDNA-1_B2377KTLT3_3.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: 93108977 total, 92750 skipped (flags/unmapped)
Fragments: 46652391 total (46285876 tlen-paired, 42826 hash-paired, 7971 singletons, 8238 discordant, 307480 orphans, 13448 too large [>5000 bp], 11671918 duplicates)
Reads: 103055869 total, 74767 skipped (flags/unmapped)
Fragments: 51658422 total (51252250 tlen-paired, 40910 hash-paired, 8631 singletons, 6256 discordant, 350375 orphans, 11632 too large [>5000 bp], 12936328 duplicates)
Reads: 104262161 total, 70789 skipped (flags/unmapped)
Fragments: 52270867 total (51837660 tlen-paired, 43030 hash-paired, 8715 singletons, 8165 discordant, 373297 orphans, 15825 too large [>5000 bp], 13127890 duplicates)
Reads: 105247924 total, 130182 skipped (flags/unmapped)
Fragments: 52916713 total (51778346 tlen-paired, 43735 hash-paired, 9041 singletons, 208414 discordant, 877177 orphans, 85267 too large [>5000 bp], 13132941 duplicates)