Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/baa313a0844db681c025755c8eebb8/.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/3a/baa313a0844db681c025755c8eebb8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_eKx-N1-BDNA-1_B23KGCJLT4_1/659_eKx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_eKx-N1-BDNA-1_B23KGCJLT4_1/659_eKx-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: 659_eKx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eKx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eKx-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eKx-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: 96251823 total, 72842 skipped (flags/unmapped)
Fragments: 48239060 total (47877627 tlen-paired, 4811 hash-paired, 410 singletons, 20605 discordant, 335607 orphans, 18439 too large [>5000 bp], 19407178 duplicates)
Reads: 102557069 total, 58390 skipped (flags/unmapped)
Fragments: 51413305 total (51005674 tlen-paired, 3316 hash-paired, 356 singletons, 17382 discordant, 386577 orphans, 29501 too large [>5000 bp], 20781006 duplicates)
Reads: 103179861 total, 56103 skipped (flags/unmapped)
Fragments: 51719005 total (51361035 tlen-paired, 3582 hash-paired, 527 singletons, 14088 discordant, 339773 orphans, 13024 too large [>5000 bp], 20325066 duplicates)
Reads: 113568415 total, 92338 skipped (flags/unmapped)
Fragments: 57029779 total (56119772 tlen-paired, 2957 hash-paired, 441 singletons, 173669 discordant, 732940 orphans, 74950 too large [>5000 bp], 23106675 duplicates)