Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/659_ekC-N1-BDNA-1_A23TY32LT4_1/659_ekC-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/e07d5d9d855d67a24ac699bf1a3388/.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/97/e07d5d9d855d67a24ac699bf1a3388/.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_ekC-N1-BDNA-1_A23TY32LT4_1/659_ekC-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: 659_ekC-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ekC-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ekC-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_ekC-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: 78620868 total, 62344 skipped (flags/unmapped)
Fragments: 39410262 total (39105663 tlen-paired, 4705 hash-paired, 390 singletons, 14626 discordant, 284878 orphans, 11634 too large [>5000 bp], 15346558 duplicates)
Reads: 84776301 total, 51380 skipped (flags/unmapped)
Fragments: 42502694 total (42190226 tlen-paired, 3603 hash-paired, 400 singletons, 10102 discordant, 298363 orphans, 9148 too large [>5000 bp], 16312380 duplicates)
Reads: 93755346 total, 99223 skipped (flags/unmapped)
Fragments: 47108286 total (46246346 tlen-paired, 2887 hash-paired, 380 singletons, 165008 discordant, 693665 orphans, 66798 too large [>5000 bp], 18405289 duplicates)
Reads: 92812943 total, 57637 skipped (flags/unmapped)
Fragments: 46532106 total (46164898 tlen-paired, 4471 hash-paired, 313 singletons, 15119 discordant, 347305 orphans, 19356 too large [>5000 bp], 18236112 duplicates)