Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/2f22d250f3ca3f1a0ea297201a760d/.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/21/2f22d250f3ca3f1a0ea297201a760d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_LWM-N1-BDNA-1_A23FG3YLT4_1/869_LWM-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0021/20260113_LH00527_0046_A23FG3YLT4__aa3fd045--20260225-014632/alignments/recalibrated/869_LWM-N1-BDNA-1_A23FG3YLT4_1/869_LWM-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
==> 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: 869_LWM-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LWM-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_LWM-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_LWM-N1-BDNA-1_A23FG3YLT4_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: 66020309 total, 45707 skipped (flags/unmapped)
Fragments: 33094839 total (32854816 tlen-paired, 3319 hash-paired, 327 singletons, 11746 discordant, 224631 orphans, 4941 too large [>5000 bp], 7655201 duplicates)
Reads: 66230313 total, 44419 skipped (flags/unmapped)
Fragments: 33198755 total (32941596 tlen-paired, 5339 hash-paired, 296 singletons, 9576 discordant, 241948 orphans, 15314 too large [>5000 bp], 7593586 duplicates)
Reads: 72488421 total, 40139 skipped (flags/unmapped)
Fragments: 36335621 total (36084113 tlen-paired, 2808 hash-paired, 433 singletons, 8372 discordant, 239895 orphans, 8684 too large [>5000 bp], 8260403 duplicates)
Reads: 73686114 total, 66211 skipped (flags/unmapped)
Fragments: 37021392 total (36371434 tlen-paired, 2650 hash-paired, 356 singletons, 123729 discordant, 523223 orphans, 50349 too large [>5000 bp], 8507332 duplicates)