Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BPR1-N1-BDNA-1_B23MHTGLT4_1/1029_BPR1-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/95afa494a4bbbfa73270e913d7339e/.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/87/95afa494a4bbbfa73270e913d7339e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_BPR1-N1-BDNA-1_B23MHTGLT4_1/1029_BPR1-N1-BDNA-1_B23MHTGLT4_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_BPR1-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BPR1-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BPR1-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BPR1-N1-BDNA-1_B23MHTGLT4_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: 78146857 total, 54550 skipped (flags/unmapped)
Fragments: 39215824 total (38841818 tlen-paired, 2913 hash-paired, 425 singletons, 13756 discordant, 356912 orphans, 8998 too large [>5000 bp], 11845856 duplicates)
Reads: 82627003 total, 46106 skipped (flags/unmapped)
Fragments: 41463219 total (41087965 tlen-paired, 2905 hash-paired, 469 singletons, 9178 discordant, 362702 orphans, 8815 too large [>5000 bp], 12279730 duplicates)
Reads: 90047430 total, 51948 skipped (flags/unmapped)
Fragments: 45191134 total (44745236 tlen-paired, 3027 hash-paired, 453 singletons, 14487 discordant, 427931 orphans, 20799 too large [>5000 bp], 13700564 duplicates)
Reads: 91106379 total, 89688 skipped (flags/unmapped)
Fragments: 45875563 total (44731601 tlen-paired, 3184 hash-paired, 481 singletons, 219879 discordant, 920418 orphans, 93232 too large [>5000 bp], 13892336 duplicates)