Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/72360d340c02495ab37c29cbe7a89d/.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/bd/72360d340c02495ab37c29cbe7a89d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1/1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1/1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> 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_BEZ8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BEZ8-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BEZ8-N1-BDNA-1_A23KFG7LT4_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: 64348167 total, 49458 skipped (flags/unmapped)
Fragments: 32337430 total (31931200 tlen-paired, 2302 hash-paired, 349 singletons, 13543 discordant, 390036 orphans, 7117 too large [>5000 bp], 11053812 duplicates)
Reads: 69012360 total, 45990 skipped (flags/unmapped)
Fragments: 34680315 total (34257140 tlen-paired, 2545 hash-paired, 324 singletons, 9230 discordant, 411076 orphans, 8570 too large [>5000 bp], 11525037 duplicates)
Reads: 76714532 total, 78303 skipped (flags/unmapped)
Fragments: 38742313 total (37427016 tlen-paired, 1457 hash-paired, 409 singletons, 258765 discordant, 1054666 orphans, 103339 too large [>5000 bp], 13166013 duplicates)
Reads: 75546054 total, 50380 skipped (flags/unmapped)
Fragments: 37963493 total (37478028 tlen-paired, 3140 hash-paired, 346 singletons, 13641 discordant, 468338 orphans, 18686 too large [>5000 bp], 12974465 duplicates)