Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_153-N1-BDNA-1_B23KFG5LT4_1/1136_153-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/63c669eac641699e733dd6a303cf3d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_153-N1-BDNA-1_B23KFG5LT4_1/1136_153-N1-BDNA-1_B23KFG5LT4_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/f0/63c669eac641699e733dd6a303cf3d/.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: 1136_153-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_153-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_153-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_153-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: 81397800 total, 62328 skipped (flags/unmapped)
Fragments: 40802173 total (40486350 tlen-paired, 2994 hash-paired, 439 singletons, 18129 discordant, 294261 orphans, 12913 too large [>5000 bp], 18075975 duplicates)
Reads: 87792960 total, 53497 skipped (flags/unmapped)
Fragments: 44008017 total (43690051 tlen-paired, 3805 hash-paired, 515 singletons, 12336 discordant, 301310 orphans, 12627 too large [>5000 bp], 19027772 duplicates)
Reads: 97473539 total, 56542 skipped (flags/unmapped)
Fragments: 48865131 total (48479068 tlen-paired, 2734 hash-paired, 343 singletons, 18514 discordant, 364472 orphans, 25775 too large [>5000 bp], 21728586 duplicates)
Reads: 98549459 total, 91018 skipped (flags/unmapped)
Fragments: 49499052 total (48669562 tlen-paired, 4135 hash-paired, 376 singletons, 156438 discordant, 668541 orphans, 64627 too large [>5000 bp], 22078366 duplicates)