Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/929ca6d0cba05680c6fcfe451fa039/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_5R3-N1-BDNA-1_A23TY32LT4_1/1029_5R3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  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/4e/929ca6d0cba05680c6fcfe451fa039/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_5R3-N1-BDNA-1_A23TY32LT4_1/1029_5R3-N1-BDNA-1_A23TY32LT4_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_5R3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5R3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5R3-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5R3-N1-BDNA-1_A23TY32LT4_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: 91722854 total, 69151 skipped (flags/unmapped)
Fragments: 46035725 total (45581684 tlen-paired, 4118 hash-paired, 412 singletons, 12230 discordant, 437281 orphans, 9973 too large [>5000 bp], 19667500 duplicates)
Reads: 100528662 total, 61732 skipped (flags/unmapped)
Fragments: 50469190 total (49960813 tlen-paired, 4093 hash-paired, 493 singletons, 8534 discordant, 495257 orphans, 12150 too large [>5000 bp], 21149302 duplicates)
Reads: 110695015 total, 121445 skipped (flags/unmapped)
Fragments: 55795821 total (54211558 tlen-paired, 4509 hash-paired, 441 singletons, 315020 discordant, 1264293 orphans, 123331 too large [>5000 bp], 23759781 duplicates)
Reads: 108937307 total, 64910 skipped (flags/unmapped)
Fragments: 54690401 total (54114948 tlen-paired, 4064 hash-paired, 377 singletons, 13622 discordant, 557390 orphans, 24681 too large [>5000 bp], 23437293 duplicates)