Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_UPJ-N1-BDNA-1_B2377KTLT3_3/869_UPJ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/ef1463dea2e945950052846b2901c7/.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/72/ef1463dea2e945950052846b2901c7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_UPJ-N1-BDNA-1_B2377KTLT3_3/869_UPJ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
==> 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_UPJ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_UPJ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_UPJ-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_UPJ-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: 45584483 total, 38740 skipped (flags/unmapped)
Fragments: 22887123 total (22634255 tlen-paired, 9535 hash-paired, 3673 singletons, 3674 discordant, 235986 orphans, 5578 too large [>5000 bp], 3645100 duplicates)
Reads: 45918611 total, 33233 skipped (flags/unmapped)
Fragments: 23066469 total (22786809 tlen-paired, 10270 hash-paired, 3679 singletons, 3364 discordant, 262347 orphans, 9233 too large [>5000 bp], 3659099 duplicates)
Reads: 50903966 total, 33560 skipped (flags/unmapped)
Fragments: 25572535 total (25275234 tlen-paired, 9799 hash-paired, 4087 singletons, 2712 discordant, 280703 orphans, 5063 too large [>5000 bp], 4070629 duplicates)
Reads: 51732898 total, 57123 skipped (flags/unmapped)
Fragments: 26127448 total (25221505 tlen-paired, 9826 hash-paired, 4225 singletons, 178906 discordant, 712986 orphans, 69045 too large [>5000 bp], 4082209 duplicates)