Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/7c438aab4efe21b317efbf580bd334/.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/44/7c438aab4efe21b317efbf580bd334/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BM6G-N1-BDNA-1_B23KFG5LT4_1/1029_BM6G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_BM6G-N1-BDNA-1_B23KFG5LT4_1/1029_BM6G-N1-BDNA-1_B23KFG5LT4_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_BM6G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BM6G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BM6G-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BM6G-N1-BDNA-1_B23KFG5LT4_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: 101036596 total, 57775 skipped (flags/unmapped)
Fragments: 50653885 total (50279936 tlen-paired, 3423 hash-paired, 454 singletons, 14337 discordant, 355735 orphans, 13620 too large [>5000 bp], 21495544 duplicates)
Reads: 94929282 total, 68715 skipped (flags/unmapped)
Fragments: 47589873 total (47217623 tlen-paired, 4196 hash-paired, 419 singletons, 20165 discordant, 347470 orphans, 14355 too large [>5000 bp], 20732892 duplicates)
Reads: 101565247 total, 66286 skipped (flags/unmapped)
Fragments: 50917160 total (50487240 tlen-paired, 5303 hash-paired, 364 singletons, 18218 discordant, 406035 orphans, 35520 too large [>5000 bp], 22145319 duplicates)
Reads: 111743062 total, 99591 skipped (flags/unmapped)
Fragments: 56135179 total (55162423 tlen-paired, 3600 hash-paired, 423 singletons, 187471 discordant, 781262 orphans, 77399 too large [>5000 bp], 24476132 duplicates)