Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/801228d439221a5af77b6f73df1e90/.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/d8/801228d439221a5af77b6f73df1e90/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_06M-N1-BDNA-1_A23NLN3LT4_1/1136_06M-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_06M-N1-BDNA-1_A23NLN3LT4_1/1136_06M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> 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_06M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_06M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_06M-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_06M-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
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: 73311682 total, 43305 skipped (flags/unmapped)
Fragments: 36759343 total (36464908 tlen-paired, 3812 hash-paired, 248 singletons, 10844 discordant, 279531 orphans, 14735 too large [>5000 bp], 12174637 duplicates)
Reads: 68318554 total, 49519 skipped (flags/unmapped)
Fragments: 34247626 total (33987748 tlen-paired, 2780 hash-paired, 253 singletons, 12741 discordant, 244104 orphans, 9070 too large [>5000 bp], 11255380 duplicates)
Reads: 73495514 total, 40603 skipped (flags/unmapped)
Fragments: 36847622 total (36580342 tlen-paired, 2077 hash-paired, 347 singletons, 8874 discordant, 255982 orphans, 7998 too large [>5000 bp], 11875683 duplicates)
Reads: 80973144 total, 70552 skipped (flags/unmapped)
Fragments: 40682295 total (39956862 tlen-paired, 2310 hash-paired, 268 singletons, 143629 discordant, 579226 orphans, 58748 too large [>5000 bp], 13479244 duplicates)