Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/4df6dd1573bee2064f662c7ab119ac/.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/6e/4df6dd1573bee2064f662c7ab119ac/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_b6o-N1-BDNA-1_B23KFG5LT4_1/659_b6o-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_b6o-N1-BDNA-1_B23KFG5LT4_1/659_b6o-N1-BDNA-1_B23KFG5LT4_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: 659_b6o-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b6o-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b6o-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b6o-N1-BDNA-1_B23KFG5LT4_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: 90070202 total, 76116 skipped (flags/unmapped)
Fragments: 45147250 total (44787126 tlen-paired, 4298 hash-paired, 483 singletons, 23310 discordant, 332033 orphans, 16051 too large [>5000 bp], 18840356 duplicates)
Reads: 97241629 total, 67707 skipped (flags/unmapped)
Fragments: 48750347 total (48357732 tlen-paired, 4921 hash-paired, 351 singletons, 19788 discordant, 367555 orphans, 20567 too large [>5000 bp], 20464887 duplicates)
Reads: 96675940 total, 61661 skipped (flags/unmapped)
Fragments: 48459787 total (48105116 tlen-paired, 2572 hash-paired, 558 singletons, 16734 discordant, 334807 orphans, 15035 too large [>5000 bp], 19811957 duplicates)
Reads: 107565874 total, 105126 skipped (flags/unmapped)
Fragments: 54005474 total (53158085 tlen-paired, 4368 hash-paired, 413 singletons, 159949 discordant, 682659 orphans, 66436 too large [>5000 bp], 22738859 duplicates)