Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_2PG-N1-BDNA-1_A23KFG7LT4_1/1029_2PG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/1dd30e938f8b4889580d59ec85ae1e/.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/f1/1dd30e938f8b4889580d59ec85ae1e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_2PG-N1-BDNA-1_A23KFG7LT4_1/1029_2PG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> 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: 1029_2PG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2PG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2PG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2PG-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: 76713804 total, 56487 skipped (flags/unmapped)
Fragments: 38546938 total (38077359 tlen-paired, 2957 hash-paired, 426 singletons, 11493 discordant, 454703 orphans, 9285 too large [>5000 bp], 14635168 duplicates)
Reads: 82889464 total, 48680 skipped (flags/unmapped)
Fragments: 41655460 total (41156664 tlen-paired, 2593 hash-paired, 456 singletons, 8359 discordant, 487388 orphans, 8854 too large [>5000 bp], 15309777 duplicates)
Reads: 81925348 total, 49894 skipped (flags/unmapped)
Fragments: 41171390 total (40645365 tlen-paired, 5132 hash-paired, 344 singletons, 10077 discordant, 510472 orphans, 21745 too large [>5000 bp], 15624766 duplicates)
Reads: 91420706 total, 80508 skipped (flags/unmapped)
Fragments: 46168489 total (44586069 tlen-paired, 2473 hash-paired, 429 singletons, 321237 discordant, 1258281 orphans, 130965 too large [>5000 bp], 17486784 duplicates)