Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/8290ed439ea1f891699206a0df3686/.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/f9/8290ed439ea1f891699206a0df3686/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_3UV-N1-BDNA-1_A23NLN3LT4_1/1136_3UV-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_3UV-N1-BDNA-1_A23NLN3LT4_1/1136_3UV-N1-BDNA-1_A23NLN3LT4_1.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: 1136_3UV-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3UV-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3UV-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3UV-N1-BDNA-1_A23NLN3LT4_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: 60289888 total, 43550 skipped (flags/unmapped)
Fragments: 30214718 total (30000318 tlen-paired, 2251 hash-paired, 308 singletons, 13143 discordant, 198698 orphans, 7954 too large [>5000 bp], 9036559 duplicates)
Reads: 65224595 total, 35913 skipped (flags/unmapped)
Fragments: 32688543 total (32473785 tlen-paired, 2252 hash-paired, 352 singletons, 9022 discordant, 203132 orphans, 7540 too large [>5000 bp], 9623883 duplicates)
Reads: 64462903 total, 38332 skipped (flags/unmapped)
Fragments: 32309149 total (32063961 tlen-paired, 3752 hash-paired, 256 singletons, 11079 discordant, 230101 orphans, 18315 too large [>5000 bp], 9759736 duplicates)
Reads: 70439126 total, 68714 skipped (flags/unmapped)
Fragments: 35357039 total (34829708 tlen-paired, 2837 hash-paired, 283 singletons, 99110 discordant, 425101 orphans, 40859 too large [>5000 bp], 10702166 duplicates)