Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BIHO-N1-BDNA-1_235YY7LT3_1/1029_BIHO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/b8b1e48caa63b19bfbd4d5f8178f62/.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/bc/b8b1e48caa63b19bfbd4d5f8178f62/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BIHO-N1-BDNA-1_235YY7LT3_1/1029_BIHO-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] [W::hts_idx_load3] The index file is older than the data file: 1029_BIHO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BIHO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1029_BIHO-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_BIHO-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: 64581851 total, 50480 skipped (flags/unmapped)
Fragments: 32414392 total (32079112 tlen-paired, 2697 hash-paired, 3929 singletons, 8216 discordant, 320438 orphans, 13477 too large [>5000 bp], 7526047 duplicates)
Reads: 64607824 total, 54935 skipped (flags/unmapped)
Fragments: 32425443 total (32104648 tlen-paired, 3522 hash-paired, 4047 singletons, 9910 discordant, 303316 orphans, 4683 too large [>5000 bp], 7607364 duplicates)
Reads: 70247556 total, 47961 skipped (flags/unmapped)
Fragments: 35259909 total (34914260 tlen-paired, 2958 hash-paired, 4265 singletons, 7034 discordant, 331392 orphans, 7717 too large [>5000 bp], 8102315 duplicates)
Reads: 71937131 total, 74591 skipped (flags/unmapped)
Fragments: 36254357 total (35251351 tlen-paired, 2820 hash-paired, 4407 singletons, 195004 discordant, 800775 orphans, 79504 too large [>5000 bp], 8377142 duplicates)