Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_IDB-N1-BDNA-1_B23L5TMLT4_1/1029_IDB-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/9d9a1c15407d423fda5fca7dc68af5/.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/9b/9d9a1c15407d423fda5fca7dc68af5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_IDB-N1-BDNA-1_B23L5TMLT4_1/1029_IDB-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_IDB-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_IDB-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1029_IDB-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_IDB-N1-BDNA-1_B23L5TMLT4_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: 86489101 total, 68619 skipped (flags/unmapped)
Fragments: 43378526 total (43001117 tlen-paired, 4868 hash-paired, 449 singletons, 15461 discordant, 356631 orphans, 10255 too large [>5000 bp], 15888241 duplicates)
Reads: 92571507 total, 59752 skipped (flags/unmapped)
Fragments: 46429523 total (46044657 tlen-paired, 3420 hash-paired, 582 singletons, 10753 discordant, 370111 orphans, 11701 too large [>5000 bp], 16763542 duplicates)
Reads: 101889259 total, 107912 skipped (flags/unmapped)
Fragments: 51251442 total (50130260 tlen-paired, 3856 hash-paired, 513 singletons, 216075 discordant, 900738 orphans, 89857 too large [>5000 bp], 18775161 duplicates)
Reads: 101192887 total, 65274 skipped (flags/unmapped)
Fragments: 50756249 total (50302846 tlen-paired, 5698 hash-paired, 488 singletons, 15922 discordant, 431295 orphans, 23449 too large [>5000 bp], 18637284 duplicates)