Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_98Q-N1-BDNA-1_B23L5TMLT4_1/1029_98Q-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/70a1c7a05b4291ed0c6e20df1d5af1/.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/96/70a1c7a05b4291ed0c6e20df1d5af1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_98Q-N1-BDNA-1_B23L5TMLT4_1/1029_98Q-N1-BDNA-1_B23L5TMLT4_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: 1029_98Q-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_98Q-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_98Q-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_98Q-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 66882259 total, 55100 skipped (flags/unmapped)
Fragments: 33558364 total (33232574 tlen-paired, 3821 hash-paired, 368 singletons, 12354 discordant, 309247 orphans, 10023 too large [>5000 bp], 12066695 duplicates)
Reads: 71837475 total, 48161 skipped (flags/unmapped)
Fragments: 36044091 total (35714233 tlen-paired, 3262 hash-paired, 438 singletons, 8270 discordant, 317888 orphans, 9729 too large [>5000 bp], 12710863 duplicates)
Reads: 78620275 total, 82375 skipped (flags/unmapped)
Fragments: 39587067 total (38598529 tlen-paired, 2769 hash-paired, 448 singletons, 189795 discordant, 795526 orphans, 79870 too large [>5000 bp], 14227462 duplicates)
Reads: 78253463 total, 52058 skipped (flags/unmapped)
Fragments: 39266436 total (38876410 tlen-paired, 3752 hash-paired, 326 singletons, 12649 discordant, 373299 orphans, 21079 too large [>5000 bp], 14138832 duplicates)