Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/54ba21f0961c7329bc8a822b9586aa/.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_D36-N1-BDNA-1_A237CFYLT3_1/869_D36-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/24/54ba21f0961c7329bc8a822b9586aa/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_D36-N1-BDNA-1_A237CFYLT3_1/869_D36-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] [W::hts_idx_load3] The index file is older than the data file: 869_D36-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_D36-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_D36-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_D36-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: 73772289 total, 94627 skipped (flags/unmapped)
Fragments: 37133289 total (36513060 tlen-paired, 7160 hash-paired, 12033 singletons, 12521 discordant, 588515 orphans, 5816 too large [>5000 bp], 7398189 duplicates)
Reads: 80646253 total, 88312 skipped (flags/unmapped)
Fragments: 40603162 total (39918176 tlen-paired, 7402 hash-paired, 12938 singletons, 9541 discordant, 655105 orphans, 9830 too large [>5000 bp], 8081563 duplicates)
Reads: 81905430 total, 91771 skipped (flags/unmapped)
Fragments: 41230445 total (40535701 tlen-paired, 7473 hash-paired, 13273 singletons, 12884 discordant, 661114 orphans, 13578 too large [>5000 bp], 8187993 duplicates)
Reads: 84659214 total, 196540 skipped (flags/unmapped)
Fragments: 42931744 total (40774178 tlen-paired, 8311 hash-paired, 13611 singletons, 418347 discordant, 1717297 orphans, 165047 too large [>5000 bp], 8400619 duplicates)