Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_7F8-N1-BDNA-1_A23H3W5LT3_1/1136_7F8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/7ed50a43256f604e5535a48b69d6b0/.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/b3/7ed50a43256f604e5535a48b69d6b0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_7F8-N1-BDNA-1_A23H3W5LT3_1/1136_7F8-N1-BDNA-1_A23H3W5LT3_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: 1136_7F8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7F8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7F8-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7F8-N1-BDNA-1_A23H3W5LT3_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: 74901535 total, 69554 skipped (flags/unmapped)
Fragments: 37566111 total (37226807 tlen-paired, 12311 hash-paired, 5171 singletons, 8314 discordant, 313508 orphans, 9219 too large [>5000 bp], 7836425 duplicates)
Reads: 82440739 total, 60769 skipped (flags/unmapped)
Fragments: 41359596 total (40968308 tlen-paired, 12281 hash-paired, 5597 singletons, 8395 discordant, 365015 orphans, 15695 too large [>5000 bp], 8555651 duplicates)
Reads: 81881862 total, 58659 skipped (flags/unmapped)
Fragments: 41079374 total (40708005 tlen-paired, 11998 hash-paired, 5461 singletons, 6186 discordant, 347724 orphans, 8820 too large [>5000 bp], 8532293 duplicates)
Reads: 84098638 total, 102543 skipped (flags/unmapped)
Fragments: 42356877 total (41244235 tlen-paired, 12778 hash-paired, 5692 singletons, 212491 discordant, 881681 orphans, 84857 too large [>5000 bp], 8720025 duplicates)