Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_VUO-N1-BDNA-1_B23L5TMLT4_1/1029_VUO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/1f81fa3ce860fea1eedcb4e6b70909/.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/24/1f81fa3ce860fea1eedcb4e6b70909/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_VUO-N1-BDNA-1_B23L5TMLT4_1/1029_VUO-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_VUO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VUO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VUO-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VUO-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: 95432378 total, 60107 skipped (flags/unmapped)
Fragments: 47879307 total (47451680 tlen-paired, 4676 hash-paired, 596 singletons, 12064 discordant, 410291 orphans, 12272 too large [>5000 bp], 18185468 duplicates)
Reads: 89117633 total, 69178 skipped (flags/unmapped)
Fragments: 44714352 total (44289005 tlen-paired, 4862 hash-paired, 481 singletons, 18154 discordant, 401850 orphans, 11041 too large [>5000 bp], 17226816 duplicates)
Reads: 104256223 total, 64941 skipped (flags/unmapped)
Fragments: 52308100 total (51794986 tlen-paired, 8370 hash-paired, 477 singletons, 18508 discordant, 485759 orphans, 30659 too large [>5000 bp], 20197681 duplicates)
Reads: 105177243 total, 104011 skipped (flags/unmapped)
Fragments: 52937525 total (51691082 tlen-paired, 3843 hash-paired, 502 singletons, 238422 discordant, 1003676 orphans, 101180 too large [>5000 bp], 20454494 duplicates)