Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/660175b0068f5dd1586b4edce0d1d1/.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/ee/660175b0068f5dd1586b4edce0d1d1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_16G-N1-BDNA-1_A23TY32LT4_1/1241_16G-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/1241_16G-N1-BDNA-1_A23TY32LT4_1/1241_16G-N1-BDNA-1_A23TY32LT4_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: 1241_16G-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_16G-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_16G-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_16G-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: 75800449 total, 55840 skipped (flags/unmapped)
Fragments: 37993137 total (37710734 tlen-paired, 4062 hash-paired, 276 singletons, 14418 discordant, 263647 orphans, 11129 too large [>5000 bp], 13460160 duplicates)
Reads: 81740254 total, 47879 skipped (flags/unmapped)
Fragments: 40974881 total (40652395 tlen-paired, 5658 hash-paired, 250 singletons, 13085 discordant, 303493 orphans, 23178 too large [>5000 bp], 14619426 duplicates)
Reads: 83173992 total, 47739 skipped (flags/unmapped)
Fragments: 41690898 total (41400332 tlen-paired, 3957 hash-paired, 334 singletons, 10304 discordant, 275971 orphans, 10381 too large [>5000 bp], 14522068 duplicates)
Reads: 90202067 total, 91790 skipped (flags/unmapped)
Fragments: 45298370 total (44537118 tlen-paired, 4970 hash-paired, 333 singletons, 146235 discordant, 609714 orphans, 61792 too large [>5000 bp], 16154698 duplicates)