Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/84eaeecd7de2104e1c6122920c5645/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_3I9-N1-BDNA-1_A237CFYLT3_1/1136_3I9-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/f4/84eaeecd7de2104e1c6122920c5645/.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_3I9-N1-BDNA-1_A237CFYLT3_1/1136_3I9-N1-BDNA-1_A237CFYLT3_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: 1136_3I9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3I9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3I9-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3I9-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: 98166895 total, 100633 skipped (flags/unmapped)
Fragments: 49279481 total (48745611 tlen-paired, 17459 hash-paired, 14951 singletons, 11445 discordant, 490015 orphans, 6133 too large [>5000 bp], 10532314 duplicates)
Reads: 106961254 total, 97828 skipped (flags/unmapped)
Fragments: 53694647 total (53113342 tlen-paired, 20342 hash-paired, 15970 singletons, 8739 discordant, 536254 orphans, 13178 too large [>5000 bp], 11450378 duplicates)
Reads: 108301215 total, 99646 skipped (flags/unmapped)
Fragments: 54367425 total (53772142 tlen-paired, 19077 hash-paired, 16247 singletons, 12305 discordant, 547654 orphans, 15310 too large [>5000 bp], 11569448 duplicates)
Reads: 110533323 total, 225754 skipped (flags/unmapped)
Fragments: 55721907 total (53961344 tlen-paired, 19953 hash-paired, 16398 singletons, 332531 discordant, 1391681 orphans, 135917 too large [>5000 bp], 11794991 duplicates)