Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/292978a589b27289009a950f9aded3/.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/f1/292978a589b27289009a950f9aded3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7NZ-N1-BDNA-1_B23KFG5LT4_1/1136_7NZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7NZ-N1-BDNA-1_B23KFG5LT4_1/1136_7NZ-N1-BDNA-1_B23KFG5LT4_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_7NZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7NZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7NZ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7NZ-N1-BDNA-1_B23KFG5LT4_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: 65515145 total, 48772 skipped (flags/unmapped)
Fragments: 32862367 total (32569137 tlen-paired, 2185 hash-paired, 303 singletons, 14018 discordant, 276724 orphans, 9333 too large [>5000 bp], 13251324 duplicates)
Reads: 70026396 total, 41248 skipped (flags/unmapped)
Fragments: 35127473 total (34829316 tlen-paired, 1970 hash-paired, 372 singletons, 9823 discordant, 285992 orphans, 8283 too large [>5000 bp], 13827348 duplicates)
Reads: 77942057 total, 48009 skipped (flags/unmapped)
Fragments: 39096580 total (38742033 tlen-paired, 4794 hash-paired, 274 singletons, 14905 discordant, 334574 orphans, 17868 too large [>5000 bp], 15825099 duplicates)
Reads: 78747056 total, 73734 skipped (flags/unmapped)
Fragments: 39607267 total (38773783 tlen-paired, 2814 hash-paired, 343 singletons, 159820 discordant, 670507 orphans, 64819 too large [>5000 bp], 16013354 duplicates)