Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_89G-N1-BDNA-1_A23NLN3LT4_1/1136_89G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_89G-N1-BDNA-1_A23NLN3LT4_1/1136_89G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/b06f10929b776dec5726f96b7b5989/.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/dc/b06f10929b776dec5726f96b7b5989/.command.run
==> 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_89G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_89G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_89G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_89G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 58382475 total, 47018 skipped (flags/unmapped)
Fragments: 29302799 total (29004606 tlen-paired, 2529 hash-paired, 258 singletons, 11009 discordant, 284397 orphans, 7257 too large [>5000 bp], 10306544 duplicates)
Reads: 62532138 total, 41800 skipped (flags/unmapped)
Fragments: 31392564 total (31053537 tlen-paired, 4875 hash-paired, 249 singletons, 9914 discordant, 323989 orphans, 14724 too large [>5000 bp], 11066011 duplicates)
Reads: 62775955 total, 39748 skipped (flags/unmapped)
Fragments: 31509162 total (31201463 tlen-paired, 1651 hash-paired, 371 singletons, 8013 discordant, 297664 orphans, 7959 too large [>5000 bp], 10796723 duplicates)
Reads: 69496653 total, 71221 skipped (flags/unmapped)
Fragments: 35001057 total (34086660 tlen-paired, 3274 hash-paired, 263 singletons, 183269 discordant, 727591 orphans, 75586 too large [>5000 bp], 12328112 duplicates)