Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_G3Y-N1-BDNA-1_B23MHTGLT4_1/1029_G3Y-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_G3Y-N1-BDNA-1_B23MHTGLT4_1/1029_G3Y-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  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/79/c4a93d85938ed785e00681ef5bea6f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/c4a93d85938ed785e00681ef5bea6f/.command.run
==> 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_G3Y-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G3Y-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G3Y-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_G3Y-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: 69010624 total, 41471 skipped (flags/unmapped)
Fragments: 34664554 total (34277064 tlen-paired, 3749 hash-paired, 311 singletons, 7538 discordant, 375892 orphans, 8124 too large [>5000 bp], 10918108 duplicates)
Reads: 65315101 total, 47158 skipped (flags/unmapped)
Fragments: 32801257 total (32439293 tlen-paired, 2417 hash-paired, 369 singletons, 8898 discordant, 350280 orphans, 8039 too large [>5000 bp], 10333245 duplicates)
Reads: 70391074 total, 39761 skipped (flags/unmapped)
Fragments: 35358966 total (34968179 tlen-paired, 1911 hash-paired, 387 singletons, 6387 discordant, 382102 orphans, 7935 too large [>5000 bp], 10788460 duplicates)
Reads: 77118256 total, 77535 skipped (flags/unmapped)
Fragments: 38907961 total (37680627 tlen-paired, 2030 hash-paired, 420 singletons, 248153 discordant, 976731 orphans, 100975 too large [>5000 bp], 12197162 duplicates)