Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_0KC-N1-BDNA-1_A237CFYLT3_1/1136_0KC-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/883cabb9d086cd4ae508b09e9cd108/.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/fe/883cabb9d086cd4ae508b09e9cd108/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_0KC-N1-BDNA-1_A237CFYLT3_1/1136_0KC-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
==> 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: 1136_0KC-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0KC-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0KC-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0KC-N1-BDNA-1_A237CFYLT3_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: 103727484 total, 112290 skipped (flags/unmapped)
Fragments: 52204930 total (51369061 tlen-paired, 12288 hash-paired, 16459 singletons, 15403 discordant, 791719 orphans, 6756 too large [>5000 bp], 13250028 duplicates)
Reads: 104700997 total, 104192 skipped (flags/unmapped)
Fragments: 52699874 total (51832857 tlen-paired, 12748 hash-paired, 16023 singletons, 13580 discordant, 824666 orphans, 18873 too large [>5000 bp], 13341131 duplicates)
Reads: 113939019 total, 108698 skipped (flags/unmapped)
Fragments: 57349271 total (56424700 tlen-paired, 15029 hash-paired, 17192 singletons, 11581 discordant, 880769 orphans, 14870 too large [>5000 bp], 14546770 duplicates)
Reads: 118671978 total, 252653 skipped (flags/unmapped)
Fragments: 60121620 total (57263296 tlen-paired, 13162 hash-paired, 18155 singletons, 567419 discordant, 2259588 orphans, 226914 too large [>5000 bp], 15062509 duplicates)