Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/535db87e72783173fa6cf29cb0284d/.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/c7/535db87e72783173fa6cf29cb0284d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_73N-N1-BDNA-1_B23MHTGLT4_1/1136_73N-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/1136_73N-N1-BDNA-1_B23MHTGLT4_1/1136_73N-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: 1136_73N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_73N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_73N-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_73N-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: 86045011 total, 61391 skipped (flags/unmapped)
Fragments: 43185988 total (42759065 tlen-paired, 3440 hash-paired, 517 singletons, 14251 discordant, 408715 orphans, 10438 too large [>5000 bp], 14068970 duplicates)
Reads: 91753100 total, 54785 skipped (flags/unmapped)
Fragments: 46046087 total (45613998 tlen-paired, 3887 hash-paired, 569 singletons, 9677 discordant, 417956 orphans, 12333 too large [>5000 bp], 14681428 duplicates)
Reads: 100923171 total, 91291 skipped (flags/unmapped)
Fragments: 50843797 total (49503792 tlen-paired, 3275 hash-paired, 525 singletons, 259546 discordant, 1076659 orphans, 110735 too large [>5000 bp], 16638217 duplicates)
Reads: 99746167 total, 56345 skipped (flags/unmapped)
Fragments: 50071712 total (49565350 tlen-paired, 4700 hash-paired, 480 singletons, 14474 discordant, 486708 orphans, 16793 too large [>5000 bp], 16383578 duplicates)