Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/a2de86dc092e9617aa403656e10f54/.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/92/a2de86dc092e9617aa403656e10f54/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_YZK-N1-BDNA-1_B23MHTGLT4_1/1029_YZK-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_YZK-N1-BDNA-1_B23MHTGLT4_1/1029_YZK-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_YZK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_YZK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_YZK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_YZK-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: 98108855 total, 77178 skipped (flags/unmapped)
Fragments: 49227727 total (48754294 tlen-paired, 4165 hash-paired, 580 singletons, 18013 discordant, 450675 orphans, 13739 too large [>5000 bp], 16757617 duplicates)
Reads: 104222101 total, 60146 skipped (flags/unmapped)
Fragments: 52298548 total (51820361 tlen-paired, 3607 hash-paired, 672 singletons, 12667 discordant, 461241 orphans, 13386 too large [>5000 bp], 17421185 duplicates)
Reads: 114623748 total, 113889 skipped (flags/unmapped)
Fragments: 57713712 total (56288572 tlen-paired, 2801 hash-paired, 613 singletons, 274218 discordant, 1147508 orphans, 115278 too large [>5000 bp], 19697836 duplicates)
Reads: 113307396 total, 66283 skipped (flags/unmapped)
Fragments: 56867207 total (56308046 tlen-paired, 3171 hash-paired, 556 singletons, 18851 discordant, 536583 orphans, 21919 too large [>5000 bp], 19414482 duplicates)