Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_OJ-N1-BDNA-1_B23MHTGLT4_1/1047_OJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/19461b6cac14fb7141c3b5e903a5d7/.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/46/19461b6cac14fb7141c3b5e903a5d7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_OJ-N1-BDNA-1_B23MHTGLT4_1/1047_OJ-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: 1047_OJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_OJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_OJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_OJ-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: 73553350 total, 43385 skipped (flags/unmapped)
Fragments: 36910918 total (36572563 tlen-paired, 2267 hash-paired, 442 singletons, 8229 discordant, 327417 orphans, 7994 too large [>5000 bp], 10785742 duplicates)
Reads: 72666970 total, 47012 skipped (flags/unmapped)
Fragments: 36470986 total (36097547 tlen-paired, 3385 hash-paired, 333 singletons, 10848 discordant, 358873 orphans, 18596 too large [>5000 bp], 10963578 duplicates)
Reads: 68712566 total, 50618 skipped (flags/unmapped)
Fragments: 34484632 total (34146300 tlen-paired, 2838 hash-paired, 455 singletons, 12260 discordant, 322779 orphans, 7959 too large [>5000 bp], 10337183 duplicates)
Reads: 80582516 total, 79361 skipped (flags/unmapped)
Fragments: 40572945 total (39554200 tlen-paired, 2446 hash-paired, 455 singletons, 201858 discordant, 813986 orphans, 85853 too large [>5000 bp], 12191239 duplicates)