Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/67291dadbbe89bfe87ec78a030fbc5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BQXQ-N1-BDNA-1_2375WFLT3_s49/1029_BQXQ-N1-BDNA-1_2375WFLT3_s49.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/b5/67291dadbbe89bfe87ec78a030fbc5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BQXQ-N1-BDNA-1_2375WFLT3_s49/1029_BQXQ-N1-BDNA-1_2375WFLT3_s49.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_BQXQ-N1-BDNA-1_2375WFLT3_s49.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQXQ-N1-BDNA-1_2375WFLT3_s49.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQXQ-N1-BDNA-1_2375WFLT3_s49.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQXQ-N1-BDNA-1_2375WFLT3_s49.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: 57450809 total, 46366 skipped (flags/unmapped)
Fragments: 28869787 total (28499466 tlen-paired, 3652 hash-paired, 821 singletons, 8866 discordant, 356982 orphans, 11336 too large [>5000 bp], 7684676 duplicates)
Reads: 56856819 total, 49380 skipped (flags/unmapped)
Fragments: 28573037 total (28211780 tlen-paired, 2952 hash-paired, 883 singletons, 10602 discordant, 346820 orphans, 4534 too large [>5000 bp], 7701729 duplicates)
Reads: 62707334 total, 43982 skipped (flags/unmapped)
Fragments: 31515362 total (31123909 tlen-paired, 2134 hash-paired, 856 singletons, 7789 discordant, 380674 orphans, 7079 too large [>5000 bp], 8316873 duplicates)
Reads: 64138701 total, 80658 skipped (flags/unmapped)
Fragments: 32402359 total (31243935 tlen-paired, 2554 hash-paired, 914 singletons, 227783 discordant, 927173 orphans, 90706 too large [>5000 bp], 8587143 duplicates)