Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/e701ed1ebc354e91361e2ada56f493/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_F5P-N1-BDNA-1_A23TY32LT4_1/1029_F5P-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  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/c4/e701ed1ebc354e91361e2ada56f493/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_F5P-N1-BDNA-1_A23TY32LT4_1/1029_F5P-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_F5P-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_F5P-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_F5P-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_F5P-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: 104728795 total, 71386 skipped (flags/unmapped)
Fragments: 52486034 total (52129564 tlen-paired, 4186 hash-paired, 350 singletons, 15497 discordant, 336437 orphans, 11064 too large [>5000 bp], 21561326 duplicates)
Reads: 113228776 total, 61822 skipped (flags/unmapped)
Fragments: 56749940 total (56375337 tlen-paired, 5724 hash-paired, 477 singletons, 11067 discordant, 357335 orphans, 12443 too large [>5000 bp], 23012239 duplicates)
Reads: 113518282 total, 62403 skipped (flags/unmapped)
Fragments: 56898400 total (56505169 tlen-paired, 5934 hash-paired, 415 singletons, 14484 discordant, 372398 orphans, 15946 too large [>5000 bp], 23573635 duplicates)
Reads: 124519453 total, 112038 skipped (flags/unmapped)
Fragments: 62533592 total (61501429 tlen-paired, 3515 hash-paired, 415 singletons, 203089 discordant, 825144 orphans, 82895 too large [>5000 bp], 25925990 duplicates)