Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/b025fb25978cb7e2dd0e1ff9f4e9a3/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_LJN-N1-BDNA-1_B23L5TMLT4_1/1029_LJN-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  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/87/b025fb25978cb7e2dd0e1ff9f4e9a3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_LJN-N1-BDNA-1_B23L5TMLT4_1/1029_LJN-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_LJN-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LJN-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LJN-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_LJN-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: 80104293 total, 65053 skipped (flags/unmapped)
Fragments: 40197281 total (39792683 tlen-paired, 4598 hash-paired, 500 singletons, 17720 discordant, 381780 orphans, 13479 too large [>5000 bp], 15119706 duplicates)
Reads: 85154386 total, 51995 skipped (flags/unmapped)
Fragments: 42734911 total (42329795 tlen-paired, 3606 hash-paired, 521 singletons, 11589 discordant, 389400 orphans, 11245 too large [>5000 bp], 15837756 duplicates)
Reads: 94016433 total, 98499 skipped (flags/unmapped)
Fragments: 47336960 total (46167822 tlen-paired, 2935 hash-paired, 493 singletons, 222933 discordant, 942777 orphans, 93642 too large [>5000 bp], 17811891 duplicates)
Reads: 93110735 total, 60249 skipped (flags/unmapped)
Fragments: 46730794 total (46254941 tlen-paired, 6536 hash-paired, 462 singletons, 17879 discordant, 450976 orphans, 20168 too large [>5000 bp], 17644116 duplicates)