Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_H5S-N1-BDNA-1_235YY7LT3_1/1029_H5S-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/0183e39391981ed94cadc101a45acd/.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/1f/0183e39391981ed94cadc101a45acd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_H5S-N1-BDNA-1_235YY7LT3_1/1029_H5S-N1-BDNA-1_235YY7LT3_1.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_H5S-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H5S-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H5S-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H5S-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: 67062703 total, 49112 skipped (flags/unmapped)
Fragments: 33634126 total (33344647 tlen-paired, 2918 hash-paired, 3454 singletons, 8414 discordant, 274693 orphans, 11743 too large [>5000 bp], 7717805 duplicates)
Reads: 60973307 total, 48345 skipped (flags/unmapped)
Fragments: 30584136 total (30320494 tlen-paired, 2974 hash-paired, 3243 singletons, 8812 discordant, 248613 orphans, 4273 too large [>5000 bp], 7095417 duplicates)
Reads: 66010028 total, 47713 skipped (flags/unmapped)
Fragments: 33106747 total (32828324 tlen-paired, 3584 hash-paired, 3454 singletons, 6168 discordant, 265217 orphans, 8746 too large [>5000 bp], 7529010 duplicates)
Reads: 67798964 total, 69971 skipped (flags/unmapped)
Fragments: 34128052 total (33318935 tlen-paired, 1868 hash-paired, 3593 singletons, 152414 discordant, 651242 orphans, 63862 too large [>5000 bp], 7808733 duplicates)