Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/2c84586b1f1c3fd9580808aacc7d18/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BGMF-N1-BDNA-1_2375WFLT3_s31/1029_BGMF-N1-BDNA-1_2375WFLT3_s31.recalibrated.bam.bai
  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/24/2c84586b1f1c3fd9580808aacc7d18/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BGMF-N1-BDNA-1_2375WFLT3_s31/1029_BGMF-N1-BDNA-1_2375WFLT3_s31.recalibrated.bam
==> 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: 1029_BGMF-N1-BDNA-1_2375WFLT3_s31.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BGMF-N1-BDNA-1_2375WFLT3_s31.recalibrated.bam.bai
The index file is older than the data file: 1029_BGMF-N1-BDNA-1_2375WFLT3_s31.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGMF-N1-BDNA-1_2375WFLT3_s31.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: 82333675 total, 67360 skipped (flags/unmapped)
Fragments: 41360307 total (40850731 tlen-paired, 3923 hash-paired, 1177 singletons, 12540 discordant, 491936 orphans, 19407 too large [>5000 bp], 12220523 duplicates)
Reads: 82098850 total, 71515 skipped (flags/unmapped)
Fragments: 41244476 total (40750501 tlen-paired, 4267 hash-paired, 1284 singletons, 15075 discordant, 473349 orphans, 6508 too large [>5000 bp], 12311760 duplicates)
Reads: 89159023 total, 64059 skipped (flags/unmapped)
Fragments: 44793964 total (44264978 tlen-paired, 3710 hash-paired, 1359 singletons, 10776 discordant, 513141 orphans, 10768 too large [>5000 bp], 13162253 duplicates)
Reads: 92261347 total, 119347 skipped (flags/unmapped)
Fragments: 46574606 total (45004209 tlen-paired, 4342 hash-paired, 1396 singletons, 308547 discordant, 1256112 orphans, 125148 too large [>5000 bp], 13698271 duplicates)