Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_D19-N1-BDNA-1_B23H2GYLT3_1/1029_D19-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/e27435c62f5e4aaf34d88b6fe3641c/.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/dd/e27435c62f5e4aaf34d88b6fe3641c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_D19-N1-BDNA-1_B23H2GYLT3_1/1029_D19-N1-BDNA-1_B23H2GYLT3_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_D19-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D19-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D19-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_D19-N1-BDNA-1_B23H2GYLT3_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: 72693370 total, 62677 skipped (flags/unmapped)
Fragments: 36468683 total (36121585 tlen-paired, 14574 hash-paired, 5538 singletons, 8507 discordant, 318479 orphans, 8672 too large [>5000 bp], 6454083 duplicates)
Reads: 72970750 total, 55749 skipped (flags/unmapped)
Fragments: 36617832 total (36248751 tlen-paired, 14428 hash-paired, 5351 singletons, 7686 discordant, 341616 orphans, 13152 too large [>5000 bp], 6443967 duplicates)
Reads: 80404496 total, 56717 skipped (flags/unmapped)
Fragments: 40348175 total (39958032 tlen-paired, 16313 hash-paired, 5933 singletons, 6305 discordant, 361592 orphans, 9477 too large [>5000 bp], 7078020 duplicates)
Reads: 81886931 total, 100432 skipped (flags/unmapped)
Fragments: 41252171 total (40129369 tlen-paired, 16326 hash-paired, 6198 singletons, 218971 discordant, 881307 orphans, 84831 too large [>5000 bp], 7197718 duplicates)