Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_YEA-N1-BDNA-1_B23KGCJLT4_1/1029_YEA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/92388a82deebfb74d46f60ea00f1e2/.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/de/92388a82deebfb74d46f60ea00f1e2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_YEA-N1-BDNA-1_B23KGCJLT4_1/1029_YEA-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_YEA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_YEA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_YEA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_YEA-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: 70186620 total, 51527 skipped (flags/unmapped)
Fragments: 35175207 total (34918265 tlen-paired, 2780 hash-paired, 447 singletons, 15067 discordant, 238648 orphans, 11887 too large [>5000 bp], 13679347 duplicates)
Reads: 75489584 total, 43038 skipped (flags/unmapped)
Fragments: 37832874 total (37581263 tlen-paired, 2588 hash-paired, 402 singletons, 10593 discordant, 238028 orphans, 9614 too large [>5000 bp], 14431518 duplicates)
Reads: 82754046 total, 48365 skipped (flags/unmapped)
Fragments: 41477838 total (41179064 tlen-paired, 3285 hash-paired, 329 singletons, 15002 discordant, 280158 orphans, 15246 too large [>5000 bp], 16269407 duplicates)
Reads: 83244361 total, 70536 skipped (flags/unmapped)
Fragments: 41794738 total (41156105 tlen-paired, 3164 hash-paired, 371 singletons, 118890 discordant, 516208 orphans, 50464 too large [>5000 bp], 16431402 duplicates)