Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/6b84f24a90278768f0dd885ed27f57/.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/d7/6b84f24a90278768f0dd885ed27f57/.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_btY-N1-BDNA-1_A23TY32LT4_1/659_btY-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_btY-N1-BDNA-1_A23TY32LT4_1/659_btY-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_btY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_btY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_btY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_btY-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: 84841387 total, 64942 skipped (flags/unmapped)
Fragments: 42526431 total (42212709 tlen-paired, 4289 hash-paired, 386 singletons, 13600 discordant, 295447 orphans, 9708 too large [>5000 bp], 16804277 duplicates)
Reads: 92072142 total, 53237 skipped (flags/unmapped)
Fragments: 46155631 total (45832308 tlen-paired, 3890 hash-paired, 450 singletons, 9498 discordant, 309485 orphans, 8789 too large [>5000 bp], 17990296 duplicates)
Reads: 101252354 total, 105376 skipped (flags/unmapped)
Fragments: 50873810 total (49945925 tlen-paired, 4450 hash-paired, 391 singletons, 177905 discordant, 745139 orphans, 72444 too large [>5000 bp], 20305714 duplicates)
Reads: 100298316 total, 58790 skipped (flags/unmapped)
Fragments: 50283463 total (49909379 tlen-paired, 4193 hash-paired, 349 singletons, 13373 discordant, 356169 orphans, 14559 too large [>5000 bp], 20074113 duplicates)