Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_4D-N1-BDNA-1_B23KGCJLT4_1/1136_4D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/2c7fa9082fb827762d49fdbe4d71ac/.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/d8/2c7fa9082fb827762d49fdbe4d71ac/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_4D-N1-BDNA-1_B23KGCJLT4_1/1136_4D-N1-BDNA-1_B23KGCJLT4_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: 1136_4D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4D-N1-BDNA-1_B23KGCJLT4_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: 69522070 total, 48926 skipped (flags/unmapped)
Fragments: 34845243 total (34593271 tlen-paired, 3712 hash-paired, 332 singletons, 12188 discordant, 235740 orphans, 9365 too large [>5000 bp], 13256533 duplicates)
Reads: 74923906 total, 41482 skipped (flags/unmapped)
Fragments: 37551912 total (37298744 tlen-paired, 2726 hash-paired, 372 singletons, 9294 discordant, 240776 orphans, 9874 too large [>5000 bp], 13991929 duplicates)
Reads: 74973669 total, 44880 skipped (flags/unmapped)
Fragments: 37583550 total (37302854 tlen-paired, 3843 hash-paired, 295 singletons, 10970 discordant, 265588 orphans, 13786 too large [>5000 bp], 14367401 duplicates)
Reads: 83070813 total, 66188 skipped (flags/unmapped)
Fragments: 41718026 total (41041416 tlen-paired, 1940 hash-paired, 343 singletons, 131595 discordant, 542732 orphans, 55824 too large [>5000 bp], 15947367 duplicates)