Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_HTI-N1-BDNA-1_B23KGCJLT4_1/1029_HTI-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/b559c4ee449507eab4bd7877dce94b/.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/09/b559c4ee449507eab4bd7877dce94b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_HTI-N1-BDNA-1_B23KGCJLT4_1/1029_HTI-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_HTI-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HTI-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HTI-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HTI-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: 60405540 total, 44177 skipped (flags/unmapped)
Fragments: 30264262 total (30069337 tlen-paired, 2548 hash-paired, 281 singletons, 10704 discordant, 181392 orphans, 7256 too large [>5000 bp], 10796984 duplicates)
Reads: 64932053 total, 38783 skipped (flags/unmapped)
Fragments: 32529528 total (32335904 tlen-paired, 2667 hash-paired, 329 singletons, 7289 discordant, 183339 orphans, 8941 too large [>5000 bp], 11350499 duplicates)
Reads: 71250439 total, 39696 skipped (flags/unmapped)
Fragments: 35701405 total (35462187 tlen-paired, 4123 hash-paired, 244 singletons, 10686 discordant, 224165 orphans, 16171 too large [>5000 bp], 12782738 duplicates)
Reads: 71159769 total, 61237 skipped (flags/unmapped)
Fragments: 35713481 total (35211902 tlen-paired, 2279 hash-paired, 311 singletons, 92870 discordant, 406119 orphans, 39000 too large [>5000 bp], 12828294 duplicates)