Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_B59-N1-BDNA-1_B23L5TMLT4_1/1029_B59-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/4bf5adcd1ca90d4a4f590698010402/.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/e3/4bf5adcd1ca90d4a4f590698010402/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_B59-N1-BDNA-1_B23L5TMLT4_1/1029_B59-N1-BDNA-1_B23L5TMLT4_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: 1029_B59-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_B59-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_B59-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_B59-N1-BDNA-1_B23L5TMLT4_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: 93501121 total, 71149 skipped (flags/unmapped)
Fragments: 46920974 total (46462306 tlen-paired, 5298 hash-paired, 465 singletons, 14914 discordant, 437991 orphans, 13240 too large [>5000 bp], 17018599 duplicates)
Reads: 99690332 total, 55057 skipped (flags/unmapped)
Fragments: 50037695 total (49562485 tlen-paired, 3256 hash-paired, 587 singletons, 10005 discordant, 461362 orphans, 10917 too large [>5000 bp], 17846105 duplicates)
Reads: 108195491 total, 64380 skipped (flags/unmapped)
Fragments: 54304952 total (53750212 tlen-paired, 8128 hash-paired, 483 singletons, 14843 discordant, 531286 orphans, 26488 too large [>5000 bp], 19760833 duplicates)
Reads: 109232276 total, 103191 skipped (flags/unmapped)
Fragments: 55035597 total (53566856 tlen-paired, 3419 hash-paired, 525 singletons, 285075 discordant, 1179722 orphans, 119069 too large [>5000 bp], 19952299 duplicates)