Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/669a087b59ace1feb3fc4e1bd552e6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_HOD-N1-BDNA-1_B23KGCJLT4_1/1029_HOD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  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/b2/669a087b59ace1feb3fc4e1bd552e6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_HOD-N1-BDNA-1_B23KGCJLT4_1/1029_HOD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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_HOD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HOD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HOD-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HOD-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: 85385232 total, 61051 skipped (flags/unmapped)
Fragments: 42818080 total (42462614 tlen-paired, 4061 hash-paired, 428 singletons, 15488 discordant, 335489 orphans, 11969 too large [>5000 bp], 18515706 duplicates)
Reads: 91270913 total, 52658 skipped (flags/unmapped)
Fragments: 45769999 total (45408052 tlen-paired, 3498 hash-paired, 597 singletons, 10886 discordant, 346966 orphans, 12910 too large [>5000 bp], 19406708 duplicates)
Reads: 100021768 total, 56394 skipped (flags/unmapped)
Fragments: 50167489 total (49726777 tlen-paired, 3388 hash-paired, 471 singletons, 16166 discordant, 420687 orphans, 25777 too large [>5000 bp], 21751202 duplicates)
Reads: 101257389 total, 84810 skipped (flags/unmapped)
Fragments: 50917714 total (49888127 tlen-paired, 2439 hash-paired, 462 singletons, 198317 discordant, 828369 orphans, 82991 too large [>5000 bp], 22072210 duplicates)