Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_5R2-N1-BDNA-1_B23MHTGLT4_1/1136_5R2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/86d63c8a4a4f6e037bd3662119bd2b/.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/7d/86d63c8a4a4f6e037bd3662119bd2b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_5R2-N1-BDNA-1_B23MHTGLT4_1/1136_5R2-N1-BDNA-1_B23MHTGLT4_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_5R2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5R2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5R2-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5R2-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: 73445168 total, 54679 skipped (flags/unmapped)
Fragments: 36861348 total (36490231 tlen-paired, 3208 hash-paired, 373 singletons, 15488 discordant, 352048 orphans, 10107 too large [>5000 bp], 11145388 duplicates)
Reads: 77433815 total, 44987 skipped (flags/unmapped)
Fragments: 38864529 total (38493640 tlen-paired, 2372 hash-paired, 530 singletons, 10379 discordant, 357608 orphans, 8954 too large [>5000 bp], 11481322 duplicates)
Reads: 84659845 total, 50440 skipped (flags/unmapped)
Fragments: 42494414 total (42064814 tlen-paired, 3177 hash-paired, 439 singletons, 15286 discordant, 410698 orphans, 15857 too large [>5000 bp], 12897412 duplicates)
Reads: 85524576 total, 81779 skipped (flags/unmapped)
Fragments: 43073661 total (41982961 tlen-paired, 2423 hash-paired, 461 singletons, 208666 discordant, 879150 orphans, 87543 too large [>5000 bp], 13079061 duplicates)