Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_56P-N1-BDNA-1_B23KGCJLT4_1/1136_56P-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/708623fe06a7d7f68b83df68e0525a/.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/99/708623fe06a7d7f68b83df68e0525a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_56P-N1-BDNA-1_B23KGCJLT4_1/1136_56P-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_56P-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_56P-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_56P-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_56P-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: 71265405 total, 52714 skipped (flags/unmapped)
Fragments: 35679823 total (35497366 tlen-paired, 3905 hash-paired, 360 singletons, 10847 discordant, 167345 orphans, 10375 too large [>5000 bp], 13027944 duplicates)
Reads: 77877257 total, 44550 skipped (flags/unmapped)
Fragments: 38993516 total (38810815 tlen-paired, 3371 hash-paired, 331 singletons, 7525 discordant, 171474 orphans, 8740 too large [>5000 bp], 14109097 duplicates)
Reads: 83586458 total, 69525 skipped (flags/unmapped)
Fragments: 41902242 total (41467317 tlen-paired, 2216 hash-paired, 330 singletons, 79424 discordant, 352955 orphans, 32867 too large [>5000 bp], 15432260 duplicates)
Reads: 83831955 total, 46958 skipped (flags/unmapped)
Fragments: 41980189 total (41742848 tlen-paired, 4458 hash-paired, 308 singletons, 11088 discordant, 221487 orphans, 23207 too large [>5000 bp], 15407967 duplicates)