Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BGI3-N1-BDNA-1_A23TNVNLT4_1/1241_BGI3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/4244f339be8c010277e68e68e74def/.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/25/4244f339be8c010277e68e68e74def/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BGI3-N1-BDNA-1_A23TNVNLT4_1/1241_BGI3-N1-BDNA-1_A23TNVNLT4_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: 1241_BGI3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BGI3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BGI3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BGI3-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: 78814658 total, 52475 skipped (flags/unmapped)
Fragments: 39516494 total (39211570 tlen-paired, 2767 hash-paired, 345 singletons, 13448 discordant, 288364 orphans, 8952 too large [>5000 bp], 14172770 duplicates)
Reads: 85153375 total, 44283 skipped (flags/unmapped)
Fragments: 42697930 total (42380759 tlen-paired, 2168 hash-paired, 450 singletons, 9771 discordant, 304782 orphans, 9232 too large [>5000 bp], 15035299 duplicates)
Reads: 84302128 total, 46950 skipped (flags/unmapped)
Fragments: 42274893 total (41935697 tlen-paired, 3639 hash-paired, 354 singletons, 12325 discordant, 322878 orphans, 14312 too large [>5000 bp], 15219453 duplicates)
Reads: 94034091 total, 89269 skipped (flags/unmapped)
Fragments: 47254783 total (46371469 tlen-paired, 3811 hash-paired, 437 singletons, 175593 discordant, 703473 orphans, 69583 too large [>5000 bp], 16965674 duplicates)