Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/8de6904e588285019746946a2296fc/.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/4d/8de6904e588285019746946a2296fc/.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_2OD-N1-BDNA-1_A23TY32LT4_1/1241_2OD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_2OD-N1-BDNA-1_A23TY32LT4_1/1241_2OD-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: 1241_2OD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_2OD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_2OD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_2OD-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: 75651720 total, 58195 skipped (flags/unmapped)
Fragments: 37967015 total (37594134 tlen-paired, 3511 hash-paired, 346 singletons, 11995 discordant, 357029 orphans, 8435 too large [>5000 bp], 15558167 duplicates)
Reads: 82103316 total, 48706 skipped (flags/unmapped)
Fragments: 41213091 total (40811255 tlen-paired, 2704 hash-paired, 385 singletons, 8610 discordant, 390137 orphans, 9475 too large [>5000 bp], 16536500 duplicates)
Reads: 81821581 total, 51698 skipped (flags/unmapped)
Fragments: 41068103 total (40646397 tlen-paired, 3620 hash-paired, 267 singletons, 10757 discordant, 407062 orphans, 20503 too large [>5000 bp], 16912835 duplicates)
Reads: 90624305 total, 97145 skipped (flags/unmapped)
Fragments: 45645863 total (44439321 tlen-paired, 3367 hash-paired, 365 singletons, 244209 discordant, 958601 orphans, 97200 too large [>5000 bp], 18670280 duplicates)