Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/6218a915ca580c9b939914c60a189a/.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/04/6218a915ca580c9b939914c60a189a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_DMZ-N1-BDNA-1_A23NLN3LT4_1/1029_DMZ-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/1029_DMZ-N1-BDNA-1_A23NLN3LT4_1/1029_DMZ-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: 1029_DMZ-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_DMZ-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DMZ-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_DMZ-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: 72154838 total, 55956 skipped (flags/unmapped)
Fragments: 36229222 total (35833573 tlen-paired, 3591 hash-paired, 347 singletons, 12522 discordant, 379189 orphans, 9987 too large [>5000 bp], 13733630 duplicates)
Reads: 77572448 total, 48259 skipped (flags/unmapped)
Fragments: 38961760 total (38505941 tlen-paired, 2525 hash-paired, 309 singletons, 10549 discordant, 442436 orphans, 21707 too large [>5000 bp], 14789373 duplicates)
Reads: 77765190 total, 46238 skipped (flags/unmapped)
Fragments: 39054385 total (38635531 tlen-paired, 2227 hash-paired, 437 singletons, 8943 discordant, 407247 orphans, 8933 too large [>5000 bp], 14408235 duplicates)
Reads: 86187605 total, 87680 skipped (flags/unmapped)
Fragments: 43453357 total (42174827 tlen-paired, 3144 hash-paired, 329 singletons, 258687 discordant, 1016370 orphans, 104955 too large [>5000 bp], 16407715 duplicates)