Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_G9U-N1-BDNA-1_A23TY32LT4_1/1029_G9U-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_G9U-N1-BDNA-1_A23TY32LT4_1/1029_G9U-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/7c725b7d2588b21690e9ffda0b9f3c/.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/9e/7c725b7d2588b21690e9ffda0b9f3c/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_G9U-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_G9U-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_G9U-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1029_G9U-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: 110277153 total, 88648 skipped (flags/unmapped)
Fragments: 55269297 total (54872145 tlen-paired, 5354 hash-paired, 500 singletons, 12111 discordant, 379187 orphans, 14799 too large [>5000 bp], 22696504 duplicates)
Reads: 119641045 total, 77478 skipped (flags/unmapped)
Fragments: 59980856 total (59492873 tlen-paired, 10465 hash-paired, 422 singletons, 10895 discordant, 466201 orphans, 34239 too large [>5000 bp], 24541768 duplicates)
Reads: 122432964 total, 75609 skipped (flags/unmapped)
Fragments: 61391036 total (60924121 tlen-paired, 5381 hash-paired, 680 singletons, 8955 discordant, 451899 orphans, 13931 too large [>5000 bp], 24753859 duplicates)
Reads: 132776109 total, 140219 skipped (flags/unmapped)
Fragments: 66750982 total (65397063 tlen-paired, 6612 hash-paired, 482 singletons, 279663 discordant, 1067162 orphans, 100785 too large [>5000 bp], 27163519 duplicates)