Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_ZEN-N1-BDNA-1_B2377KTLT3_3/869_ZEN-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_ZEN-N1-BDNA-1_B2377KTLT3_3/869_ZEN-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/1a7cf86d405d7c8aaecf42bf83ff75/.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/a0/1a7cf86d405d7c8aaecf42bf83ff75/.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: 869_ZEN-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_ZEN-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 53604244 total, 56062 skipped (flags/unmapped)
Fragments: 26922554 total (26593288 tlen-paired, 11752 hash-paired, 3798 singletons, 4880 discordant, 308836 orphans, 7854 too large [>5000 bp], 4857419 duplicates)
Reads: 59801967 total, 44776 skipped (flags/unmapped)
Fragments: 30054187 total (29676789 tlen-paired, 11090 hash-paired, 4200 singletons, 3673 discordant, 358435 orphans, 5726 too large [>5000 bp], 5403381 duplicates)
Reads: 54065382 total, 42943 skipped (flags/unmapped)
Fragments: 27171993 total (26814530 tlen-paired, 12992 hash-paired, 3649 singletons, 4592 discordant, 336230 orphans, 9166 too large [>5000 bp], 4883794 duplicates)
Reads: 60747673 total, 77759 skipped (flags/unmapped)
Fragments: 30705036 total (29543128 tlen-paired, 10845 hash-paired, 4299 singletons, 228589 discordant, 918175 orphans, 91158 too large [>5000 bp], 5439933 duplicates)