Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_IBG-N1-BDNA-1_B23KFG5LT4_1/1029_IBG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/618fcefa75300b487ef908cc382ec0/.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/db/618fcefa75300b487ef908cc382ec0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_IBG-N1-BDNA-1_B23KFG5LT4_1/1029_IBG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_IBG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_IBG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IBG-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_IBG-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: 67621551 total, 50844 skipped (flags/unmapped)
Fragments: 33876766 total (33666516 tlen-paired, 2533 hash-paired, 320 singletons, 10070 discordant, 197327 orphans, 7411 too large [>5000 bp], 13730106 duplicates)
Reads: 73365483 total, 41335 skipped (flags/unmapped)
Fragments: 36758855 total (36540891 tlen-paired, 2210 hash-paired, 348 singletons, 7424 discordant, 207982 orphans, 7384 too large [>5000 bp], 14528537 duplicates)
Reads: 74145036 total, 43582 skipped (flags/unmapped)
Fragments: 37146955 total (36920663 tlen-paired, 2730 hash-paired, 310 singletons, 8998 discordant, 214254 orphans, 11054 too large [>5000 bp], 15127662 duplicates)
Reads: 81497065 total, 70034 skipped (flags/unmapped)
Fragments: 40899739 total (40319345 tlen-paired, 2438 hash-paired, 310 singletons, 113127 discordant, 464519 orphans, 46191 too large [>5000 bp], 16684809 duplicates)