Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/548f2df0e0ed57f99451f552e13fa8/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BPLF-N1-BDNA-1_235YY7LT3_1/1029_BPLF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/548f2df0e0ed57f99451f552e13fa8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BPLF-N1-BDNA-1_235YY7LT3_1/1029_BPLF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BPLF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BPLF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BPLF-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BPLF-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 51326188 total, 42455 skipped (flags/unmapped)
Fragments: 25752912 total (25511870 tlen-paired, 3094 hash-paired, 2754 singletons, 7513 discordant, 227681 orphans, 4172 too large [>5000 bp], 5452216 duplicates)
Reads: 51510851 total, 40098 skipped (flags/unmapped)
Fragments: 25845242 total (25591197 tlen-paired, 2886 hash-paired, 2786 singletons, 6474 discordant, 241899 orphans, 12477 too large [>5000 bp], 5409655 duplicates)
Reads: 56251287 total, 38244 skipped (flags/unmapped)
Fragments: 28225213 total (27967410 tlen-paired, 2601 hash-paired, 3078 singletons, 5407 discordant, 246717 orphans, 6206 too large [>5000 bp], 5855590 duplicates)
Reads: 57237022 total, 63646 skipped (flags/unmapped)
Fragments: 28824213 total (28082603 tlen-paired, 2282 hash-paired, 3072 singletons, 143520 discordant, 592736 orphans, 60379 too large [>5000 bp], 6021240 duplicates)