Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_P6B-N1-BDNA-1_A237CFYLT3_1/869_P6B-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/306af2f55f8063474942ec46828ce4/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_P6B-N1-BDNA-1_A237CFYLT3_1/869_P6B-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  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/e6/306af2f55f8063474942ec46828ce4/.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_P6B-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_P6B-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_P6B-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_P6B-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: 70684198 total, 80775 skipped (flags/unmapped)
Fragments: 35525417 total (35047638 tlen-paired, 11521 hash-paired, 12151 singletons, 8899 discordant, 445208 orphans, 4974 too large [>5000 bp], 6771311 duplicates)
Reads: 77788090 total, 80447 skipped (flags/unmapped)
Fragments: 39097551 total (38555620 tlen-paired, 12714 hash-paired, 12800 singletons, 9518 discordant, 506899 orphans, 16120 too large [>5000 bp], 7402693 duplicates)
Reads: 76727522 total, 74182 skipped (flags/unmapped)
Fragments: 38568313 total (38049026 tlen-paired, 12606 hash-paired, 12683 singletons, 6339 discordant, 487659 orphans, 8528 too large [>5000 bp], 7335930 duplicates)
Reads: 80624718 total, 174255 skipped (flags/unmapped)
Fragments: 40751419 total (39117664 tlen-paired, 12856 hash-paired, 13388 singletons, 316094 discordant, 1291417 orphans, 126215 too large [>5000 bp], 7633758 duplicates)