Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_73Z-N1-BDNA-1_A23NLN3LT4_1/1136_73Z-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/d04c381410a06921218d32dd8dc70b/.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/25/d04c381410a06921218d32dd8dc70b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_73Z-N1-BDNA-1_A23NLN3LT4_1/1136_73Z-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_73Z-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_73Z-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_73Z-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_73Z-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: 90589270 total, 62513 skipped (flags/unmapped)
Fragments: 45390734 total (45096807 tlen-paired, 3324 hash-paired, 370 singletons, 15388 discordant, 274845 orphans, 10252 too large [>5000 bp], 15725663 duplicates)
Reads: 97562526 total, 52697 skipped (flags/unmapped)
Fragments: 48886572 total (48587488 tlen-paired, 3440 hash-paired, 483 singletons, 11069 discordant, 284092 orphans, 10630 too large [>5000 bp], 16656226 duplicates)
Reads: 107134876 total, 96486 skipped (flags/unmapped)
Fragments: 53771310 total (52993394 tlen-paired, 3313 hash-paired, 427 singletons, 146149 discordant, 628027 orphans, 62112 too large [>5000 bp], 18805199 duplicates)
Reads: 106268982 total, 58597 skipped (flags/unmapped)
Fragments: 53254289 total (52883187 tlen-paired, 3534 hash-paired, 401 singletons, 16521 discordant, 350646 orphans, 26427 too large [>5000 bp], 18578527 duplicates)