Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_II5-N1-BDNA-1_A23NMNVLT4_1/1029_II5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/782b401188f36a621de8cd058bebdb/.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/4c/782b401188f36a621de8cd058bebdb/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_II5-N1-BDNA-1_A23NMNVLT4_1/1029_II5-N1-BDNA-1_A23NMNVLT4_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_II5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_II5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_II5-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_II5-N1-BDNA-1_A23NMNVLT4_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: 65791488 total, 39690 skipped (flags/unmapped)
Fragments: 32962581 total (32764047 tlen-paired, 2525 hash-paired, 282 singletons, 10837 discordant, 184890 orphans, 5904 too large [>5000 bp], 7838693 duplicates)
Reads: 70527569 total, 36795 skipped (flags/unmapped)
Fragments: 35338361 total (35109991 tlen-paired, 4107 hash-paired, 204 singletons, 9425 discordant, 214634 orphans, 14445 too large [>5000 bp], 8520374 duplicates)
Reads: 71585177 total, 35210 skipped (flags/unmapped)
Fragments: 35862865 total (35662354 tlen-paired, 2391 hash-paired, 340 singletons, 7653 discordant, 190127 orphans, 7352 too large [>5000 bp], 8349930 duplicates)
Reads: 77904996 total, 58960 skipped (flags/unmapped)
Fragments: 39090934 total (38570827 tlen-paired, 2193 hash-paired, 348 singletons, 99260 discordant, 418306 orphans, 41411 too large [>5000 bp], 9465171 duplicates)