Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_48S-N1-BDNA-1_B23KFG5LT4_1/1136_48S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/e56afc438d08e59a5271a494ed7a93/.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/4f/e56afc438d08e59a5271a494ed7a93/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_48S-N1-BDNA-1_B23KFG5LT4_1/1136_48S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_48S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_48S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_48S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_48S-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: 76707133 total, 57453 skipped (flags/unmapped)
Fragments: 38445170 total (38163437 tlen-paired, 2892 hash-paired, 272 singletons, 14671 discordant, 263898 orphans, 11755 too large [>5000 bp], 14998045 duplicates)
Reads: 81513194 total, 47572 skipped (flags/unmapped)
Fragments: 40856110 total (40574960 tlen-paired, 3681 hash-paired, 368 singletons, 9769 discordant, 267332 orphans, 10551 too large [>5000 bp], 15601012 duplicates)
Reads: 90503767 total, 87241 skipped (flags/unmapped)
Fragments: 45453756 total (44701165 tlen-paired, 3142 hash-paired, 391 singletons, 141263 discordant, 607795 orphans, 58600 too large [>5000 bp], 17818445 duplicates)
Reads: 90046805 total, 53012 skipped (flags/unmapped)
Fragments: 45140422 total (44783490 tlen-paired, 4905 hash-paired, 326 singletons, 15836 discordant, 335865 orphans, 24570 too large [>5000 bp], 17658281 duplicates)