Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_DFS-N1-BDNA-1_B2377KTLT3_3/869_DFS-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/c438dfa55ba3af7edeb04a669ae53b/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_DFS-N1-BDNA-1_B2377KTLT3_3/869_DFS-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/c438dfa55ba3af7edeb04a669ae53b/.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_DFS-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_DFS-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DFS-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_DFS-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: 77312360 total, 70392 skipped (flags/unmapped)
Fragments: 38940928 total (38267056 tlen-paired, 7012 hash-paired, 6904 singletons, 7142 discordant, 652814 orphans, 9915 too large [>5000 bp], 9664840 duplicates)
Reads: 77982372 total, 59642 skipped (flags/unmapped)
Fragments: 39303068 total (38570552 tlen-paired, 8694 hash-paired, 6786 singletons, 6594 discordant, 710442 orphans, 16911 too large [>5000 bp], 9716706 duplicates)
Reads: 85333853 total, 62530 skipped (flags/unmapped)
Fragments: 43012361 total (42225874 tlen-paired, 8088 hash-paired, 7288 singletons, 5848 discordant, 765263 orphans, 9576 too large [>5000 bp], 10662515 duplicates)
Reads: 88636309 total, 113888 skipped (flags/unmapped)
Fragments: 45063949 total (42544239 tlen-paired, 9218 hash-paired, 7774 singletons, 504209 discordant, 1998509 orphans, 200403 too large [>5000 bp], 10898037 duplicates)