Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1136_5O9-N1-BDNA-1_A23TY32LT4_1/1136_5O9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/2189b7e9bd8e81396be8fb43ad7529/.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/b0/2189b7e9bd8e81396be8fb43ad7529/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1136_5O9-N1-BDNA-1_A23TY32LT4_1/1136_5O9-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: 1136_5O9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5O9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5O9-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5O9-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: 73682467 total, 56647 skipped (flags/unmapped)
Fragments: 36919275 total (36674102 tlen-paired, 4242 hash-paired, 351 singletons, 9893 discordant, 230687 orphans, 9154 too large [>5000 bp], 13831541 duplicates)
Reads: 79430818 total, 45388 skipped (flags/unmapped)
Fragments: 39807310 total (39552393 tlen-paired, 2532 hash-paired, 308 singletons, 6775 discordant, 245302 orphans, 8210 too large [>5000 bp], 14646154 duplicates)
Reads: 86791992 total, 50734 skipped (flags/unmapped)
Fragments: 43497879 total (43202554 tlen-paired, 4037 hash-paired, 286 singletons, 10468 discordant, 280534 orphans, 13160 too large [>5000 bp], 16353599 duplicates)
Reads: 87714728 total, 86183 skipped (flags/unmapped)
Fragments: 44052796 total (43310799 tlen-paired, 3167 hash-paired, 309 singletons, 144539 discordant, 593982 orphans, 58622 too large [>5000 bp], 16545711 duplicates)