Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2PU-N1-BDNA-1_A237CFYLT3_1/1136_2PU-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/dbc8abb75684bc44a52a2be2f492af/.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/0e/dbc8abb75684bc44a52a2be2f492af/.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_2PU-N1-BDNA-1_A237CFYLT3_1/1136_2PU-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2PU-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2PU-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2PU-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2PU-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: 63921315 total, 64964 skipped (flags/unmapped)
Fragments: 32598032 total (31227722 tlen-paired, 3622 hash-paired, 9727 singletons, 6793 discordant, 1350168 orphans, 10091 too large [>5000 bp], 7129786 duplicates)
Reads: 63119222 total, 69027 skipped (flags/unmapped)
Fragments: 32178067 total (30852786 tlen-paired, 3085 hash-paired, 9825 singletons, 7517 discordant, 1304854 orphans, 4370 too large [>5000 bp], 7088185 duplicates)
Reads: 69151838 total, 64943 skipped (flags/unmapped)
Fragments: 35275811 total (33786963 tlen-paired, 3161 hash-paired, 10551 singletons, 5960 discordant, 1469176 orphans, 7500 too large [>5000 bp], 7671876 duplicates)
Reads: 76093260 total, 150183 skipped (flags/unmapped)
Fragments: 39579152 total (34505199 tlen-paired, 2583 hash-paired, 11242 singletons, 1038739 discordant, 4021389 orphans, 408702 too large [>5000 bp], 8321894 duplicates)