Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_QZ1-N1-BDNA-1_B23KFG5LT4_1/1029_QZ1-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_QZ1-N1-BDNA-1_B23KFG5LT4_1/1029_QZ1-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/b526a4860b416feac42030be50d59a/.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/eb/b526a4860b416feac42030be50d59a/.command.run
==> 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_QZ1-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_QZ1-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_QZ1-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_QZ1-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: 68153404 total, 50894 skipped (flags/unmapped)
Fragments: 34160550 total (33907716 tlen-paired, 2620 hash-paired, 276 singletons, 14194 discordant, 235744 orphans, 8715 too large [>5000 bp], 12981742 duplicates)
Reads: 74435681 total, 40579 skipped (flags/unmapped)
Fragments: 37310779 total (37055660 tlen-paired, 1600 hash-paired, 301 singletons, 10143 discordant, 243075 orphans, 8460 too large [>5000 bp], 13869233 duplicates)
Reads: 74625744 total, 45184 skipped (flags/unmapped)
Fragments: 37409655 total (37115004 tlen-paired, 4005 hash-paired, 257 singletons, 12458 discordant, 277931 orphans, 19719 too large [>5000 bp], 14330760 duplicates)
Reads: 82230362 total, 76949 skipped (flags/unmapped)
Fragments: 41289838 total (40631129 tlen-paired, 2366 hash-paired, 303 singletons, 126652 discordant, 529388 orphans, 51714 too large [>5000 bp], 15869751 duplicates)