Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_5OV-N1-BDNA-1_A23MHW3LT4_1/1029_5OV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/6844e13f0e0de80c7cf53957754634/.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/ec/6844e13f0e0de80c7cf53957754634/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_5OV-N1-BDNA-1_A23MHW3LT4_1/1029_5OV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> 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_5OV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5OV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5OV-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_5OV-N1-BDNA-1_A23MHW3LT4_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: 74031234 total, 59282 skipped (flags/unmapped)
Fragments: 37176085 total (36752577 tlen-paired, 3159 hash-paired, 494 singletons, 16289 discordant, 403566 orphans, 11921 too large [>5000 bp], 11635762 duplicates)
Reads: 85957039 total, 54612 skipped (flags/unmapped)
Fragments: 43170069 total (42671282 tlen-paired, 6522 hash-paired, 475 singletons, 16156 discordant, 475634 orphans, 19199 too large [>5000 bp], 13531043 duplicates)
Reads: 77401703 total, 48987 skipped (flags/unmapped)
Fragments: 38868481 total (38449619 tlen-paired, 2140 hash-paired, 553 singletons, 11412 discordant, 404757 orphans, 10532 too large [>5000 bp], 11905783 duplicates)
Reads: 85376746 total, 85404 skipped (flags/unmapped)
Fragments: 43051851 total (41786200 tlen-paired, 1906 hash-paired, 503 singletons, 238593 discordant, 1024649 orphans, 106396 too large [>5000 bp], 13462100 duplicates)