Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_JC4-N1-BDNA-1_A23TY32LT4_1/1241_JC4-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/3cd558c0d723d237a8f0c73a5b2403/.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/d5/3cd558c0d723d237a8f0c73a5b2403/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_JC4-N1-BDNA-1_A23TY32LT4_1/1241_JC4-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: 1241_JC4-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_JC4-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_JC4-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_JC4-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: 67187141 total, 49343 skipped (flags/unmapped)
Fragments: 33692638 total (33415177 tlen-paired, 3113 hash-paired, 333 singletons, 10876 discordant, 263139 orphans, 7997 too large [>5000 bp], 12756018 duplicates)
Reads: 72283506 total, 41755 skipped (flags/unmapped)
Fragments: 36253186 total (35965688 tlen-paired, 2431 hash-paired, 391 singletons, 7666 discordant, 277010 orphans, 6390 too large [>5000 bp], 13585056 duplicates)
Reads: 80359928 total, 85380 skipped (flags/unmapped)
Fragments: 40409061 total (39561003 tlen-paired, 3201 hash-paired, 308 singletons, 165737 discordant, 678812 orphans, 67773 too large [>5000 bp], 15452814 duplicates)
Reads: 79607041 total, 45529 skipped (flags/unmapped)
Fragments: 39927254 total (39595158 tlen-paired, 3921 hash-paired, 248 singletons, 11903 discordant, 316024 orphans, 11638 too large [>5000 bp], 15297990 duplicates)