Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_d1e-N1-BDNA-1_A23TY32LT4_1/659_d1e-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/36d2c157b655926414cb2d82b0e921/.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/46/36d2c157b655926414cb2d82b0e921/.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_d1e-N1-BDNA-1_A23TY32LT4_1/659_d1e-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] [W::hts_idx_load3] The index file is older than the data file: 659_d1e-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_d1e-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_d1e-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_d1e-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: 92914161 total, 67547 skipped (flags/unmapped)
Fragments: 46578206 total (46227699 tlen-paired, 4778 hash-paired, 369 singletons, 13959 discordant, 331401 orphans, 10986 too large [>5000 bp], 18458201 duplicates)
Reads: 99548517 total, 55115 skipped (flags/unmapped)
Fragments: 49909934 total (49550728 tlen-paired, 3882 hash-paired, 532 singletons, 9566 discordant, 345226 orphans, 9646 too large [>5000 bp], 19564439 duplicates)
Reads: 110698697 total, 112307 skipped (flags/unmapped)
Fragments: 55631253 total (54577850 tlen-paired, 4981 hash-paired, 393 singletons, 204942 discordant, 843087 orphans, 83682 too large [>5000 bp], 22181053 duplicates)
Reads: 109115741 total, 60899 skipped (flags/unmapped)
Fragments: 54707264 total (54276576 tlen-paired, 5262 hash-paired, 319 singletons, 15222 discordant, 409885 orphans, 25259 too large [>5000 bp], 21850371 duplicates)