Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B2HF-N1-BDNA-1_A23TNVNLT4_1/1241_B2HF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/056e01a480aa8bd7e96c2df88490a7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B2HF-N1-BDNA-1_A23TNVNLT4_1/1241_B2HF-N1-BDNA-1_A23TNVNLT4_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/84/056e01a480aa8bd7e96c2df88490a7/.command.run
==> 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_B2HF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_B2HF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_B2HF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B2HF-N1-BDNA-1_A23TNVNLT4_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: 74008304 total, 50887 skipped (flags/unmapped)
Fragments: 37099096 total (36826839 tlen-paired, 2116 hash-paired, 443 singletons, 12836 discordant, 256862 orphans, 8265 too large [>5000 bp], 13535015 duplicates)
Reads: 79575742 total, 45793 skipped (flags/unmapped)
Fragments: 39892162 total (39603173 tlen-paired, 4357 hash-paired, 342 singletons, 11241 discordant, 273049 orphans, 9508 too large [>5000 bp], 14656257 duplicates)
Reads: 88165185 total, 85718 skipped (flags/unmapped)
Fragments: 44288271 total (43512932 tlen-paired, 3219 hash-paired, 373 singletons, 153337 discordant, 618410 orphans, 60854 too large [>5000 bp], 16251002 duplicates)
Reads: 80621694 total, 44127 skipped (flags/unmapped)
Fragments: 40415081 total (40132877 tlen-paired, 1952 hash-paired, 468 singletons, 9235 discordant, 270549 orphans, 9211 too large [>5000 bp], 14463630 duplicates)