Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/9cc11c27d33253468f16bd53309b53/.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/8c/9cc11c27d33253468f16bd53309b53/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_G71-N1-BDNA-1_B2377KTLT3_1/869_G71-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_G71-N1-BDNA-1_B2377KTLT3_1/869_G71-N1-BDNA-1_B2377KTLT3_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_G71-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_G71-N1-BDNA-1_B2377KTLT3_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: 98291903 total, 83454 skipped (flags/unmapped)
Fragments: 49355609 total (48812227 tlen-paired, 21427 hash-paired, 6983 singletons, 8812 discordant, 506160 orphans, 5187 too large [>5000 bp], 11720992 duplicates)
Reads: 107184667 total, 79689 skipped (flags/unmapped)
Fragments: 53841096 total (53211105 tlen-paired, 24855 hash-paired, 7373 singletons, 6250 discordant, 591513 orphans, 10836 too large [>5000 bp], 12794298 duplicates)
Reads: 108796679 total, 80897 skipped (flags/unmapped)
Fragments: 54639638 total (54004869 tlen-paired, 22851 hash-paired, 7514 singletons, 8800 discordant, 595604 orphans, 19812 too large [>5000 bp], 12955832 duplicates)
Reads: 111750828 total, 149899 skipped (flags/unmapped)
Fragments: 56429397 total (54474687 tlen-paired, 24761 hash-paired, 7831 singletons, 383234 discordant, 1538884 orphans, 144425 too large [>5000 bp], 13254151 duplicates)