Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/4c62d2489ccb8355e545daa2cf2208/.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/2e/4c62d2489ccb8355e545daa2cf2208/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BS4O-N1-BDNA-1_B23L5TMLT4_1/1029_BS4O-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BS4O-N1-BDNA-1_B23L5TMLT4_1/1029_BS4O-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_BS4O-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BS4O-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BS4O-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BS4O-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: 81648636 total, 50225 skipped (flags/unmapped)
Fragments: 40970984 total (40593872 tlen-paired, 3838 hash-paired, 475 singletons, 11579 discordant, 361220 orphans, 9069 too large [>5000 bp], 14374710 duplicates)
Reads: 76548119 total, 61547 skipped (flags/unmapped)
Fragments: 38411423 total (38035029 tlen-paired, 4518 hash-paired, 513 singletons, 16958 discordant, 354405 orphans, 9322 too large [>5000 bp], 13689766 duplicates)
Reads: 90395148 total, 93608 skipped (flags/unmapped)
Fragments: 45495128 total (44421413 tlen-paired, 4169 hash-paired, 399 singletons, 205510 discordant, 863637 orphans, 87660 too large [>5000 bp], 16239518 duplicates)
Reads: 89319435 total, 56563 skipped (flags/unmapped)
Fragments: 44824459 total (44373156 tlen-paired, 4547 hash-paired, 451 singletons, 17416 discordant, 428889 orphans, 21647 too large [>5000 bp], 16006187 duplicates)