Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/be8ce33c3a0dbf8b1f6b57defe2d64/.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/3d/be8ce33c3a0dbf8b1f6b57defe2d64/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_TB0-N1-BDNA-1_A23H3NYLT3_1/869_TB0-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_TB0-N1-BDNA-1_A23H3NYLT3_1/869_TB0-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
==> 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_TB0-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_TB0-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_TB0-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_TB0-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: 77366470 total, 60967 skipped (flags/unmapped)
Fragments: 38807334 total (38456387 tlen-paired, 18945 hash-paired, 7386 singletons, 7101 discordant, 317515 orphans, 7868 too large [>5000 bp], 4970380 duplicates)
Reads: 84317434 total, 56113 skipped (flags/unmapped)
Fragments: 42308176 total (41908040 tlen-paired, 18818 hash-paired, 7770 singletons, 5667 discordant, 367881 orphans, 10310 too large [>5000 bp], 5368255 duplicates)
Reads: 84430974 total, 92371 skipped (flags/unmapped)
Fragments: 42546798 total (41379395 tlen-paired, 19002 hash-paired, 7942 singletons, 222196 discordant, 918263 orphans, 85606 too large [>5000 bp], 5375296 duplicates)
Reads: 83555052 total, 58952 skipped (flags/unmapped)
Fragments: 41919027 total (41517381 tlen-paired, 19381 hash-paired, 7960 singletons, 7305 discordant, 367000 orphans, 16503 too large [>5000 bp], 5327303 duplicates)