Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/32d059ab0dd571a4ad918a03ee1a43/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_PME-N1-BDNA-1_B23L5TMLT4_1/1029_PME-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_PME-N1-BDNA-1_B23L5TMLT4_1/1029_PME-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/c4/32d059ab0dd571a4ad918a03ee1a43/.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_PME-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PME-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PME-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_PME-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: 82307713 total, 69369 skipped (flags/unmapped)
Fragments: 41302117 total (40890271 tlen-paired, 4716 hash-paired, 477 singletons, 17264 discordant, 389389 orphans, 11988 too large [>5000 bp], 15868084 duplicates)
Reads: 88524226 total, 57083 skipped (flags/unmapped)
Fragments: 44420310 total (44004758 tlen-paired, 4167 hash-paired, 502 singletons, 11996 discordant, 398887 orphans, 12956 too large [>5000 bp], 16739902 duplicates)
Reads: 95841958 total, 64243 skipped (flags/unmapped)
Fragments: 48098448 total (47606404 tlen-paired, 6821 hash-paired, 464 singletons, 18272 discordant, 466487 orphans, 23885 too large [>5000 bp], 18505040 duplicates)
Reads: 96347322 total, 98845 skipped (flags/unmapped)
Fragments: 48514189 total (47310834 tlen-paired, 3852 hash-paired, 500 singletons, 229436 discordant, 969567 orphans, 95083 too large [>5000 bp], 18631069 duplicates)