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/f7/27d2db8afa27f9122e893144d1ba22/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/27d2db8afa27f9122e893144d1ba22/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_HPO-N1-BDNA-1_B23MHTGLT4_1/1029_HPO-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_HPO-N1-BDNA-1_B23MHTGLT4_1/1029_HPO-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] [W::hts_idx_load3] The index file is older than the data file: 1029_HPO-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_HPO-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HPO-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HPO-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: 71589563 total, 55637 skipped (flags/unmapped)
Fragments: 35944198 total (35556790 tlen-paired, 3480 hash-paired, 519 singletons, 12064 discordant, 371345 orphans, 8697 too large [>5000 bp], 9960656 duplicates)
Reads: 76622175 total, 43661 skipped (flags/unmapped)
Fragments: 38471810 total (38078883 tlen-paired, 2966 hash-paired, 530 singletons, 7683 discordant, 381748 orphans, 8586 too large [>5000 bp], 10509607 duplicates)
Reads: 84213633 total, 81598 skipped (flags/unmapped)
Fragments: 42465820 total (41216832 tlen-paired, 2860 hash-paired, 529 singletons, 243137 discordant, 1002462 orphans, 101693 too large [>5000 bp], 11834417 duplicates)
Reads: 83174916 total, 51256 skipped (flags/unmapped)
Fragments: 41765974 total (41298032 tlen-paired, 5353 hash-paired, 503 singletons, 12345 discordant, 449741 orphans, 20978 too large [>5000 bp], 11673792 duplicates)