Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_5CB-N1-BDNA-1_A23KFG7LT4_1/1029_5CB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/67866bbe3c6991b1ec370d4ecb9620/.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/1c/67866bbe3c6991b1ec370d4ecb9620/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_5CB-N1-BDNA-1_A23KFG7LT4_1/1029_5CB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_5CB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_5CB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5CB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5CB-N1-BDNA-1_A23KFG7LT4_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: 66530951 total, 47807 skipped (flags/unmapped)
Fragments: 33408566 total (33047257 tlen-paired, 2861 hash-paired, 408 singletons, 7736 discordant, 350304 orphans, 8362 too large [>5000 bp], 12141817 duplicates)
Reads: 71965379 total, 41129 skipped (flags/unmapped)
Fragments: 36147615 total (35753462 tlen-paired, 1948 hash-paired, 381 singletons, 5851 discordant, 385973 orphans, 7687 too large [>5000 bp], 12705305 duplicates)
Reads: 71386501 total, 41978 skipped (flags/unmapped)
Fragments: 35854590 total (35443980 tlen-paired, 4354 hash-paired, 293 singletons, 6939 discordant, 399024 orphans, 17330 too large [>5000 bp], 12994199 duplicates)
Reads: 79595457 total, 73236 skipped (flags/unmapped)
Fragments: 40157211 total (38896715 tlen-paired, 1869 hash-paired, 374 singletons, 258756 discordant, 999497 orphans, 103835 too large [>5000 bp], 14507530 duplicates)