Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_LSE-N1-BDNA-1_A23H3NYLT3_1/869_LSE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_LSE-N1-BDNA-1_A23H3NYLT3_1/869_LSE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/172c112dea3e5ad928a916cf52c97e/.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/e8/172c112dea3e5ad928a916cf52c97e/.command.run
==> 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: 869_LSE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LSE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LSE-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LSE-N1-BDNA-1_A23H3NYLT3_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: 113412294 total, 94949 skipped (flags/unmapped)
Fragments: 56900148 total (56351371 tlen-paired, 27891 hash-paired, 11518 singletons, 10525 discordant, 498843 orphans, 13705 too large [>5000 bp], 9800555 duplicates)
Reads: 122637789 total, 89558 skipped (flags/unmapped)
Fragments: 61547391 total (60922711 tlen-paired, 28364 hash-paired, 12326 singletons, 11193 discordant, 572797 orphans, 19286 too large [>5000 bp], 10511177 duplicates)
Reads: 122615741 total, 83774 skipped (flags/unmapped)
Fragments: 61546545 total (60925500 tlen-paired, 27696 hash-paired, 12148 singletons, 8484 discordant, 572717 orphans, 11871 too large [>5000 bp], 10506624 duplicates)
Reads: 124418073 total, 153815 skipped (flags/unmapped)
Fragments: 62725174 total (60884336 tlen-paired, 28418 hash-paired, 12399 singletons, 352320 discordant, 1447701 orphans, 137005 too large [>5000 bp], 10625626 duplicates)