Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_L2B-N1-BDNA-1_B23L5TMLT4_1/1029_L2B-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/e3cf972d98451dd6717a478d2e0ae0/.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/d9/e3cf972d98451dd6717a478d2e0ae0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_L2B-N1-BDNA-1_B23L5TMLT4_1/1029_L2B-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> 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_L2B-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_L2B-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_L2B-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_L2B-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: 79013926 total, 64807 skipped (flags/unmapped)
Fragments: 39632660 total (39274078 tlen-paired, 4517 hash-paired, 518 singletons, 14694 discordant, 338853 orphans, 11585 too large [>5000 bp], 14568271 duplicates)
Reads: 83997326 total, 52102 skipped (flags/unmapped)
Fragments: 42136310 total (41776343 tlen-paired, 3774 hash-paired, 534 singletons, 9861 discordant, 345798 orphans, 9468 too large [>5000 bp], 15209770 duplicates)
Reads: 91698808 total, 61134 skipped (flags/unmapped)
Fragments: 46000557 total (45577793 tlen-paired, 7289 hash-paired, 481 singletons, 14707 discordant, 400287 orphans, 18664 too large [>5000 bp], 16970652 duplicates)
Reads: 92764359 total, 94302 skipped (flags/unmapped)
Fragments: 46677042 total (45615873 tlen-paired, 3441 hash-paired, 468 singletons, 204093 discordant, 853167 orphans, 84804 too large [>5000 bp], 17166059 duplicates)