Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_bGc-N1-BDNA-1_B23KFG5LT4_1/659_bGc-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/56b39d4211862981b108dfb8738f60/.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/87/56b39d4211862981b108dfb8738f60/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_bGc-N1-BDNA-1_B23KFG5LT4_1/659_bGc-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: 659_bGc-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_bGc-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-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: 68036873 total, 58225 skipped (flags/unmapped)
Fragments: 34093353 total (33848944 tlen-paired, 3400 hash-paired, 267 singletons, 16031 discordant, 224711 orphans, 8460 too large [>5000 bp], 13369014 duplicates)
Reads: 74858378 total, 48759 skipped (flags/unmapped)
Fragments: 37509722 total (37267542 tlen-paired, 3077 hash-paired, 355 singletons, 10712 discordant, 228036 orphans, 9283 too large [>5000 bp], 14542208 duplicates)
Reads: 81651443 total, 52918 skipped (flags/unmapped)
Fragments: 40920271 total (40620326 tlen-paired, 6321 hash-paired, 267 singletons, 16397 discordant, 276960 orphans, 17605 too large [>5000 bp], 16281648 duplicates)
Reads: 82247139 total, 82213 skipped (flags/unmapped)
Fragments: 41275225 total (40690319 tlen-paired, 2824 hash-paired, 305 singletons, 108366 discordant, 473411 orphans, 44096 too large [>5000 bp], 16453011 duplicates)