Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_C3-N1-BDNA-1_B23L5TMLT4_1/1047_C3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/aafbb0ae6f85097c1665c6575e91ef/.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/bd/aafbb0ae6f85097c1665c6575e91ef/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_C3-N1-BDNA-1_B23L5TMLT4_1/1047_C3-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] The index file is older than the data file: 1047_C3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_C3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_C3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_C3-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: 81858298 total, 66726 skipped (flags/unmapped)
Fragments: 41105124 total (40647395 tlen-paired, 3882 hash-paired, 463 singletons, 15955 discordant, 437429 orphans, 9608 too large [>5000 bp], 14370902 duplicates)
Reads: 87263753 total, 57489 skipped (flags/unmapped)
Fragments: 43820121 total (43348276 tlen-paired, 3489 hash-paired, 558 singletons, 11122 discordant, 456676 orphans, 11628 too large [>5000 bp], 15111147 duplicates)
Reads: 94595340 total, 59875 skipped (flags/unmapped)
Fragments: 47505394 total (46964589 tlen-paired, 4640 hash-paired, 492 singletons, 16278 discordant, 519395 orphans, 22282 too large [>5000 bp], 16703344 duplicates)
Reads: 95761894 total, 106479 skipped (flags/unmapped)
Fragments: 48288048 total (46860141 tlen-paired, 3703 hash-paired, 504 singletons, 277123 discordant, 1146577 orphans, 113200 too large [>5000 bp], 16885220 duplicates)