Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_OVG-N1-BDNA-1_A23MHW3LT4_1/1029_OVG-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/774f800565bd337f2c195829457daa/.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/69/774f800565bd337f2c195829457daa/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_OVG-N1-BDNA-1_A23MHW3LT4_1/1029_OVG-N1-BDNA-1_A23MHW3LT4_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_OVG-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_OVG-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_OVG-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_OVG-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: 75640640 total, 60906 skipped (flags/unmapped)
Fragments: 38000269 total (37536139 tlen-paired, 3388 hash-paired, 460 singletons, 16406 discordant, 443876 orphans, 11766 too large [>5000 bp], 13074062 duplicates)
Reads: 80131418 total, 51212 skipped (flags/unmapped)
Fragments: 40256973 total (39785420 tlen-paired, 3078 hash-paired, 525 singletons, 11309 discordant, 456641 orphans, 11713 too large [>5000 bp], 13633992 duplicates)
Reads: 87455272 total, 58817 skipped (flags/unmapped)
Fragments: 43940579 total (43399204 tlen-paired, 4958 hash-paired, 502 singletons, 16588 discordant, 519327 orphans, 17563 too large [>5000 bp], 15162982 duplicates)
Reads: 88294451 total, 86795 skipped (flags/unmapped)
Fragments: 44568770 total (43129469 tlen-paired, 3378 hash-paired, 507 singletons, 277095 discordant, 1158321 orphans, 114472 too large [>5000 bp], 15344365 duplicates)