Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_65R-N1-BDNA-1_A23H3NYLT3_1/1136_65R-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/530381303e1406d4273543c8d75bbc/.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/48/530381303e1406d4273543c8d75bbc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_65R-N1-BDNA-1_A23H3NYLT3_1/1136_65R-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_65R-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1136_65R-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_65R-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1136_65R-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: 81604954 total, 64988 skipped (flags/unmapped)
Fragments: 40977992 total (40498701 tlen-paired, 21557 hash-paired, 8573 singletons, 7212 discordant, 441949 orphans, 17252 too large [>5000 bp], 5933894 duplicates)
Reads: 82501608 total, 72625 skipped (flags/unmapped)
Fragments: 41413627 total (40957215 tlen-paired, 22435 hash-paired, 8826 singletons, 8056 discordant, 417095 orphans, 13825 too large [>5000 bp], 6044522 duplicates)
Reads: 90727584 total, 105192 skipped (flags/unmapped)
Fragments: 45801884 total (44269231 tlen-paired, 22191 hash-paired, 9423 singletons, 302792 discordant, 1198247 orphans, 113147 too large [>5000 bp], 6549409 duplicates)
Reads: 90553762 total, 64686 skipped (flags/unmapped)
Fragments: 45480553 total (44953107 tlen-paired, 24140 hash-paired, 9373 singletons, 6666 discordant, 487267 orphans, 12305 too large [>5000 bp], 6541882 duplicates)