Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_BK-N1-BDNA-1_A23TNVNLT4_1/1267_BK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/cbefba50a78b37ec3f24ac47395231/.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/cbefba50a78b37ec3f24ac47395231/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_BK-N1-BDNA-1_A23TNVNLT4_1/1267_BK-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: 1267_BK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BK-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_BK-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: 73845699 total, 47800 skipped (flags/unmapped)
Fragments: 37028892 total (36744753 tlen-paired, 2386 hash-paired, 379 singletons, 7730 discordant, 273644 orphans, 7069 too large [>5000 bp], 14625946 duplicates)
Reads: 78591076 total, 42297 skipped (flags/unmapped)
Fragments: 39414627 total (39110039 tlen-paired, 1948 hash-paired, 423 singletons, 5631 discordant, 296586 orphans, 8267 too large [>5000 bp], 15361939 duplicates)
Reads: 88318334 total, 82480 skipped (flags/unmapped)
Fragments: 44426361 total (43457163 tlen-paired, 3671 hash-paired, 386 singletons, 195171 discordant, 769970 orphans, 76744 too large [>5000 bp], 17582732 duplicates)
Reads: 86724883 total, 46109 skipped (flags/unmapped)
Fragments: 43491799 total (43135092 tlen-paired, 4966 hash-paired, 334 singletons, 8187 discordant, 343220 orphans, 19365 too large [>5000 bp], 17290519 duplicates)