Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_K8V-N1-BDNA-1_A237CFYLT3_1/869_K8V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/a688b4a93e9f9ec232c20be4778d90/.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/0d/a688b4a93e9f9ec232c20be4778d90/.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_K8V-N1-BDNA-1_A237CFYLT3_1/869_K8V-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: 869_K8V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K8V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K8V-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_K8V-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: 83743042 total, 74571 skipped (flags/unmapped)
Fragments: 42168284 total (41467827 tlen-paired, 6958 hash-paired, 11276 singletons, 6472 discordant, 675751 orphans, 9465 too large [>5000 bp], 8579412 duplicates)
Reads: 84967732 total, 77043 skipped (flags/unmapped)
Fragments: 42777774 total (42079112 tlen-paired, 6232 hash-paired, 11480 singletons, 8323 discordant, 672627 orphans, 9624 too large [>5000 bp], 8692371 duplicates)
Reads: 76624224 total, 81734 skipped (flags/unmapped)
Fragments: 38571871 total (37943744 tlen-paired, 6432 hash-paired, 10799 singletons, 8981 discordant, 601915 orphans, 5731 too large [>5000 bp], 7878328 duplicates)
Reads: 87900206 total, 178714 skipped (flags/unmapped)
Fragments: 44601110 total (42313619 tlen-paired, 5009 hash-paired, 11894 singletons, 450482 discordant, 1820106 orphans, 175636 too large [>5000 bp], 8924110 duplicates)