Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b82007c9b25206e0d5269e8b6522ac/.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/03/b82007c9b25206e0d5269e8b6522ac/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BK3C-N1-BDNA-1_A23MHW3LT4_1/1029_BK3C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_BK3C-N1-BDNA-1_A23MHW3LT4_1/1029_BK3C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BK3C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BK3C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BK3C-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BK3C-N1-BDNA-1_A23MHW3LT4_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: 82634138 total, 63995 skipped (flags/unmapped)
Fragments: 41579799 total (40952216 tlen-paired, 3802 hash-paired, 666 singletons, 14724 discordant, 608391 orphans, 9801 too large [>5000 bp], 15000109 duplicates)
Reads: 87814586 total, 56881 skipped (flags/unmapped)
Fragments: 44186738 total (43532295 tlen-paired, 3034 hash-paired, 602 singletons, 10250 discordant, 640557 orphans, 12694 too large [>5000 bp], 15586898 duplicates)
Reads: 95679589 total, 62450 skipped (flags/unmapped)
Fragments: 48148083 total (47417231 tlen-paired, 5965 hash-paired, 515 singletons, 14680 discordant, 709692 orphans, 15590 too large [>5000 bp], 17411162 duplicates)
Reads: 97858827 total, 100633 skipped (flags/unmapped)
Fragments: 49568020 total (47411204 tlen-paired, 3144 hash-paired, 611 singletons, 425124 discordant, 1727937 orphans, 175351 too large [>5000 bp], 17731548 duplicates)