Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_0W2-N1-BDNA-1_B23KGCJLT4_1/1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/3e50e93d44d5b76a99f47f6caaf4ec/.command.sh
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/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/93/3e50e93d44d5b76a99f47f6caaf4ec/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_0W2-N1-BDNA-1_B23KGCJLT4_1/1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-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: 68105654 total, 56114 skipped (flags/unmapped)
Fragments: 34124211 total (33891253 tlen-paired, 3559 hash-paired, 359 singletons, 10095 discordant, 218945 orphans, 10211 too large [>5000 bp], 13111082 duplicates)
Reads: 74186879 total, 46140 skipped (flags/unmapped)
Fragments: 37180127 total (36928895 tlen-paired, 2970 hash-paired, 402 singletons, 7263 discordant, 240597 orphans, 10742 too large [>5000 bp], 13903234 duplicates)
Reads: 73219172 total, 48079 skipped (flags/unmapped)
Fragments: 36697642 total (36439086 tlen-paired, 5068 hash-paired, 316 singletons, 8067 discordant, 245105 orphans, 10615 too large [>5000 bp], 14061337 duplicates)
Reads: 81014859 total, 82147 skipped (flags/unmapped)
Fragments: 40685746 total (39997484 tlen-paired, 2479 hash-paired, 360 singletons, 136643 discordant, 548780 orphans, 55180 too large [>5000 bp], 15554602 duplicates)