Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_HV2-N1-BDNA-1_A237CFYLT3_1/869_HV2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_HV2-N1-BDNA-1_A237CFYLT3_1/869_HV2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/e8b3164e0a351a6ba2dba857bc4130/.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/7b/e8b3164e0a351a6ba2dba857bc4130/.command.run
==> 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_HV2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_HV2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_HV2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_HV2-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: 84047161 total, 92307 skipped (flags/unmapped)
Fragments: 42260233 total (41664487 tlen-paired, 7933 hash-paired, 12426 singletons, 10903 discordant, 564484 orphans, 5649 too large [>5000 bp], 8786957 duplicates)
Reads: 93095133 total, 87628 skipped (flags/unmapped)
Fragments: 46813149 total (46144538 tlen-paired, 11223 hash-paired, 13042 singletons, 11955 discordant, 632391 orphans, 13320 too large [>5000 bp], 9664757 duplicates)
Reads: 92013260 total, 84598 skipped (flags/unmapped)
Fragments: 46271238 total (45619715 tlen-paired, 7543 hash-paired, 12951 singletons, 7884 discordant, 623145 orphans, 11141 too large [>5000 bp], 9589604 duplicates)
Reads: 96389619 total, 200314 skipped (flags/unmapped)
Fragments: 48765550 total (46687544 tlen-paired, 7808 hash-paired, 13575 singletons, 405895 discordant, 1650728 orphans, 161254 too large [>5000 bp], 9951538 duplicates)