Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_3FA-N1-BDNA-1_A237CFYLT3_1/1136_3FA-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/2be86299acd03fa04b6e38927e429e/.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/1e/2be86299acd03fa04b6e38927e429e/.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_3FA-N1-BDNA-1_A237CFYLT3_1/1136_3FA-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_3FA-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3FA-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3FA-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3FA-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: 67543163 total, 68120 skipped (flags/unmapped)
Fragments: 33976286 total (33463887 tlen-paired, 7920 hash-paired, 9029 singletons, 9442 discordant, 486008 orphans, 8754 too large [>5000 bp], 6531357 duplicates)
Reads: 66909467 total, 74127 skipped (flags/unmapped)
Fragments: 33657708 total (33149964 tlen-paired, 7874 hash-paired, 9125 singletons, 10668 discordant, 480077 orphans, 4563 too large [>5000 bp], 6490013 duplicates)
Reads: 73135871 total, 70665 skipped (flags/unmapped)
Fragments: 36790986 total (36241791 tlen-paired, 7889 hash-paired, 9830 singletons, 7868 discordant, 523608 orphans, 8336 too large [>5000 bp], 7059241 duplicates)
Reads: 75477984 total, 170079 skipped (flags/unmapped)
Fragments: 38194322 total (36507137 tlen-paired, 8699 hash-paired, 10077 singletons, 328407 discordant, 1340002 orphans, 134670 too large [>5000 bp], 7264578 duplicates)