Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1/1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/f9d6d3b23e4d995783a72f7d3d4967/.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/2b/f9d6d3b23e4d995783a72f7d3d4967/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1/1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
==> 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_BJ1D-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJ1D-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJ1D-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: 104750113 total, 73702 skipped (flags/unmapped)
Fragments: 52530682 total (52093413 tlen-paired, 4580 hash-paired, 459 singletons, 20652 discordant, 411578 orphans, 13542 too large [>5000 bp], 20860068 duplicates)
Reads: 112063167 total, 62243 skipped (flags/unmapped)
Fragments: 56208414 total (55730698 tlen-paired, 5715 hash-paired, 441 singletons, 17309 discordant, 454251 orphans, 19394 too large [>5000 bp], 22476712 duplicates)
Reads: 111928801 total, 63142 skipped (flags/unmapped)
Fragments: 56136127 total (55686489 tlen-paired, 3855 hash-paired, 530 singletons, 14580 discordant, 430673 orphans, 12304 too large [>5000 bp], 21927295 duplicates)
Reads: 124337049 total, 119658 skipped (flags/unmapped)
Fragments: 62506629 total (61262665 tlen-paired, 4248 hash-paired, 518 singletons, 246831 discordant, 992367 orphans, 98509 too large [>5000 bp], 24967051 duplicates)