Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/71e94d40868ce58edc405f58b8e313/.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/32/71e94d40868ce58edc405f58b8e313/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1029_NXR-N1-BDNA-1_A23H3W5LT3_1/1029_NXR-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1029_NXR-N1-BDNA-1_A23H3W5LT3_1/1029_NXR-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_NXR-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_NXR-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_NXR-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_NXR-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: 62076994 total, 54005 skipped (flags/unmapped)
Fragments: 31225001 total (30772070 tlen-paired, 4787 hash-paired, 4093 singletons, 6635 discordant, 437416 orphans, 7248 too large [>5000 bp], 6172640 duplicates)
Reads: 68104308 total, 45681 skipped (flags/unmapped)
Fragments: 34275703 total (33757893 tlen-paired, 5661 hash-paired, 4443 singletons, 4800 discordant, 502906 orphans, 7285 too large [>5000 bp], 6744544 duplicates)
Reads: 68613732 total, 48428 skipped (flags/unmapped)
Fragments: 34526535 total (34000120 tlen-paired, 6161 hash-paired, 4448 singletons, 6480 discordant, 509326 orphans, 13004 too large [>5000 bp], 6790327 duplicates)
Reads: 70934075 total, 82214 skipped (flags/unmapped)
Fragments: 35966809 total (34288232 tlen-paired, 5947 hash-paired, 4718 singletons, 332853 discordant, 1335059 orphans, 129010 too large [>5000 bp], 6951162 duplicates)