Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_BNK6-N1-BDNA-1_A23H3NYLT3_1/1029_BNK6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/8f73daef092c12ad7d22934de629d4/.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/a1/8f73daef092c12ad7d22934de629d4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1029_BNK6-N1-BDNA-1_A23H3NYLT3_1/1029_BNK6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
==> 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: 1029_BNK6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BNK6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNK6-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BNK6-N1-BDNA-1_A23H3NYLT3_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: 66165072 total, 53303 skipped (flags/unmapped)
Fragments: 33180192 total (32896799 tlen-paired, 17518 hash-paired, 7084 singletons, 5084 discordant, 253707 orphans, 6088 too large [>5000 bp], 4123170 duplicates)
Reads: 71842045 total, 47002 skipped (flags/unmapped)
Fragments: 36039953 total (35716437 tlen-paired, 18381 hash-paired, 7444 singletons, 4388 discordant, 293303 orphans, 7942 too large [>5000 bp], 4434003 duplicates)
Reads: 71498637 total, 50961 skipped (flags/unmapped)
Fragments: 35860353 total (35542810 tlen-paired, 18306 hash-paired, 7374 singletons, 5357 discordant, 286506 orphans, 10425 too large [>5000 bp], 4418302 duplicates)
Reads: 72442537 total, 84853 skipped (flags/unmapped)
Fragments: 36480086 total (35541753 tlen-paired, 17906 hash-paired, 7758 singletons, 179279 discordant, 733390 orphans, 69330 too large [>5000 bp], 4465160 duplicates)