Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/a28cadba7ef1a833a15477fe6ce7f3/.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/e4/a28cadba7ef1a833a15477fe6ce7f3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_eyD-N1-BDNA-1_A23TY32LT4_1/659_eyD-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/659_eyD-N1-BDNA-1_A23TY32LT4_1/659_eyD-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: 659_eyD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eyD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eyD-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eyD-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: 71366479 total, 53638 skipped (flags/unmapped)
Fragments: 35805285 total (35474346 tlen-paired, 4181 hash-paired, 308 singletons, 9453 discordant, 316997 orphans, 9788 too large [>5000 bp], 14260083 duplicates)
Reads: 77411702 total, 47558 skipped (flags/unmapped)
Fragments: 38846192 total (38467432 tlen-paired, 4200 hash-paired, 272 singletons, 8750 discordant, 365538 orphans, 18785 too large [>5000 bp], 15610880 duplicates)
Reads: 78449188 total, 46973 skipped (flags/unmapped)
Fragments: 39367892 total (39007227 tlen-paired, 4018 hash-paired, 365 singletons, 7058 discordant, 349224 orphans, 8010 too large [>5000 bp], 15421729 duplicates)
Reads: 86176730 total, 88485 skipped (flags/unmapped)
Fragments: 43390065 total (42290514 tlen-paired, 3958 hash-paired, 359 singletons, 223272 discordant, 871962 orphans, 90218 too large [>5000 bp], 17345138 duplicates)