Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_20-N1-BDNA-1_A23NLN3LT4_1/1136_20-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/96ff0eea44b521663e2504c3c18dc1/.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/f4/96ff0eea44b521663e2504c3c18dc1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_20-N1-BDNA-1_A23NLN3LT4_1/1136_20-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> 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: 1136_20-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_20-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_20-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_20-N1-BDNA-1_A23NLN3LT4_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: 83330427 total, 59682 skipped (flags/unmapped)
Fragments: 41765542 total (41463096 tlen-paired, 3609 hash-paired, 403 singletons, 17564 discordant, 280870 orphans, 10467 too large [>5000 bp], 14885211 duplicates)
Reads: 89260183 total, 53949 skipped (flags/unmapped)
Fragments: 44742292 total (44411804 tlen-paired, 3838 hash-paired, 284 singletons, 15134 discordant, 311232 orphans, 16583 too large [>5000 bp], 16072448 duplicates)
Reads: 89874980 total, 49263 skipped (flags/unmapped)
Fragments: 45046177 total (44743021 tlen-paired, 3082 hash-paired, 361 singletons, 12397 discordant, 287316 orphans, 10520 too large [>5000 bp], 15754655 duplicates)
Reads: 98112671 total, 89248 skipped (flags/unmapped)
Fragments: 49256740 total (48503022 tlen-paired, 3840 hash-paired, 308 singletons, 142165 discordant, 607405 orphans, 58828 too large [>5000 bp], 17720350 duplicates)