Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/0ef05330e7049a0b23e98fe611d34b/.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/06/0ef05330e7049a0b23e98fe611d34b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_4CO-N1-BDNA-1_A23NLN3LT4_1/1136_4CO-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_4CO-N1-BDNA-1_A23NLN3LT4_1/1136_4CO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> 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: 1136_4CO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4CO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4CO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4CO-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: 86627293 total, 58265 skipped (flags/unmapped)
Fragments: 43399177 total (43133611 tlen-paired, 3260 hash-paired, 372 singletons, 15430 discordant, 246504 orphans, 8775 too large [>5000 bp], 14721250 duplicates)
Reads: 93480716 total, 47414 skipped (flags/unmapped)
Fragments: 46830951 total (46566828 tlen-paired, 3128 hash-paired, 443 singletons, 10665 discordant, 249887 orphans, 10865 too large [>5000 bp], 15687968 duplicates)
Reads: 102096779 total, 55170 skipped (flags/unmapped)
Fragments: 51150314 total (50809526 tlen-paired, 5274 hash-paired, 351 singletons, 16363 discordant, 318800 orphans, 30066 too large [>5000 bp], 17528230 duplicates)
Reads: 102739590 total, 91250 skipped (flags/unmapped)
Fragments: 51540716 total (50871884 tlen-paired, 3989 hash-paired, 356 singletons, 123687 discordant, 540800 orphans, 54032 too large [>5000 bp], 17718217 duplicates)