Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8d420e782c0efd1edce1d88fc65aaf/.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/4b/8d420e782c0efd1edce1d88fc65aaf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_KVO-N1-BDNA-1_B23MHTGLT4_1/1029_KVO-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_KVO-N1-BDNA-1_B23MHTGLT4_1/1029_KVO-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_KVO-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KVO-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KVO-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KVO-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: 88423531 total, 60097 skipped (flags/unmapped)
Fragments: 44472859 total (43847260 tlen-paired, 4195 hash-paired, 553 singletons, 13936 discordant, 606915 orphans, 12592 too large [>5000 bp], 13967749 duplicates)
Reads: 83295908 total, 73745 skipped (flags/unmapped)
Fragments: 41896823 total (41276852 tlen-paired, 5516 hash-paired, 511 singletons, 20068 discordant, 593876 orphans, 11452 too large [>5000 bp], 13406751 duplicates)
Reads: 98840698 total, 99110 skipped (flags/unmapped)
Fragments: 50000027 total (48032922 tlen-paired, 3484 hash-paired, 560 singletons, 385077 discordant, 1577984 orphans, 160039 too large [>5000 bp], 16032329 duplicates)
Reads: 96640498 total, 65157 skipped (flags/unmapped)
Fragments: 48614822 total (47900121 tlen-paired, 3925 hash-paired, 482 singletons, 20763 discordant, 689531 orphans, 17855 too large [>5000 bp], 15652792 duplicates)