Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BA1G-N1-BDNA-1_A23KFG7LT4_1/1029_BA1G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BA1G-N1-BDNA-1_A23KFG7LT4_1/1029_BA1G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/f404f7c7717f3516ff2bc09976c0e6/.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/8d/f404f7c7717f3516ff2bc09976c0e6/.command.run
==> 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: 1029_BA1G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BA1G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BA1G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BA1G-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: 70492868 total, 49435 skipped (flags/unmapped)
Fragments: 35348591 total (35063123 tlen-paired, 2588 hash-paired, 304 singletons, 7823 discordant, 274753 orphans, 10654 too large [>5000 bp], 12398402 duplicates)
Reads: 76214855 total, 42641 skipped (flags/unmapped)
Fragments: 38229989 total (37913412 tlen-paired, 2708 hash-paired, 393 singletons, 5887 discordant, 307589 orphans, 10109 too large [>5000 bp], 13064826 duplicates)
Reads: 82496865 total, 43840 skipped (flags/unmapped)
Fragments: 41379070 total (41043311 tlen-paired, 2220 hash-paired, 286 singletons, 7538 discordant, 325715 orphans, 10443 too large [>5000 bp], 14464934 duplicates)
Reads: 83257279 total, 74754 skipped (flags/unmapped)
Fragments: 41906623 total (40928736 tlen-paired, 1810 hash-paired, 366 singletons, 192774 discordant, 782937 orphans, 76291 too large [>5000 bp], 14611741 duplicates)