Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BNG8-N1-BDNA-1_235YY7LT3_1/1029_BNG8-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/5412fc348b5e42de4c23aaaf68dfcf/.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/c7/5412fc348b5e42de4c23aaaf68dfcf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BNG8-N1-BDNA-1_235YY7LT3_1/1029_BNG8-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
==> 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_BNG8-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNG8-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNG8-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNG8-N1-BDNA-1_235YY7LT3_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: 42033567 total, 45221 skipped (flags/unmapped)
Fragments: 21282738 total (20691646 tlen-paired, 2433 hash-paired, 2322 singletons, 4703 discordant, 581634 orphans, 3413 too large [>5000 bp], 5629875 duplicates)
Reads: 44687395 total, 43981 skipped (flags/unmapped)
Fragments: 22637505 total (21989000 tlen-paired, 1863 hash-paired, 2231 singletons, 3550 discordant, 640861 orphans, 5748 too large [>5000 bp], 5817095 duplicates)
Reads: 46455483 total, 47398 skipped (flags/unmapped)
Fragments: 23524625 total (22853335 tlen-paired, 3870 hash-paired, 2405 singletons, 4671 discordant, 660344 orphans, 10792 too large [>5000 bp], 6127168 duplicates)
Reads: 48437004 total, 69952 skipped (flags/unmapped)
Fragments: 24911398 total (22653845 tlen-paired, 1459 hash-paired, 2628 singletons, 443868 discordant, 1809598 orphans, 178241 too large [>5000 bp], 6226651 duplicates)