Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/849ff4cf6341b542a0c589bfda8467/.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/65/849ff4cf6341b542a0c589bfda8467/.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_83S-N1-BDNA-1_A23TY32LT4_1/1136_83S-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/1136_83S-N1-BDNA-1_A23TY32LT4_1/1136_83S-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_83S-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_83S-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_83S-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_83S-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: 53940036 total, 40180 skipped (flags/unmapped)
Fragments: 27028946 total (26848978 tlen-paired, 2385 hash-paired, 244 singletons, 6667 discordant, 170672 orphans, 6440 too large [>5000 bp], 10210221 duplicates)
Reads: 59001735 total, 33691 skipped (flags/unmapped)
Fragments: 29571581 total (29377484 tlen-paired, 2382 hash-paired, 231 singletons, 4819 discordant, 186665 orphans, 5889 too large [>5000 bp], 10954800 duplicates)
Reads: 58280425 total, 34380 skipped (flags/unmapped)
Fragments: 29209445 total (29009816 tlen-paired, 2839 hash-paired, 204 singletons, 5791 discordant, 190795 orphans, 9077 too large [>5000 bp], 11087145 duplicates)
Reads: 64303188 total, 64088 skipped (flags/unmapped)
Fragments: 32295649 total (31741931 tlen-paired, 2793 hash-paired, 267 singletons, 110603 discordant, 440055 orphans, 44062 too large [>5000 bp], 12239579 duplicates)