Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/a1c2fd3fc3894f676994d75372d0c1/.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/53/a1c2fd3fc3894f676994d75372d0c1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_34-N1-BDNA-1_B2377KTLT3_1/869_34-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_34-N1-BDNA-1_B2377KTLT3_1/869_34-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] [W::hts_idx_load3] The index file is older than the data file: 869_34-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 869_34-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_34-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_34-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: 49210428 total, 43004 skipped (flags/unmapped)
Fragments: 24783619 total (24369037 tlen-paired, 4547 hash-paired, 4162 singletons, 3913 discordant, 401960 orphans, 3154 too large [>5000 bp], 4062023 duplicates)
Reads: 54138500 total, 41279 skipped (flags/unmapped)
Fragments: 27284218 total (26795044 tlen-paired, 4687 hash-paired, 4424 singletons, 2920 discordant, 477143 orphans, 5176 too large [>5000 bp], 4477029 duplicates)
Reads: 55086434 total, 43645 skipped (flags/unmapped)
Fragments: 27750742 total (27261327 tlen-paired, 5918 hash-paired, 4562 singletons, 4384 discordant, 474551 orphans, 10209 too large [>5000 bp], 4530807 duplicates)
Reads: 56909239 total, 77419 skipped (flags/unmapped)
Fragments: 28940804 total (27322744 tlen-paired, 4626 hash-paired, 4806 singletons, 323688 discordant, 1284940 orphans, 119979 too large [>5000 bp], 4607088 duplicates)