Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/6fee3a18cdc5d82622d23ff929cdc4/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7Q4-N1-BDNA-1_A23NLN3LT4_1/1136_7Q4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  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/69/6fee3a18cdc5d82622d23ff929cdc4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7Q4-N1-BDNA-1_A23NLN3LT4_1/1136_7Q4-N1-BDNA-1_A23NLN3LT4_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: 1136_7Q4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q4-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7Q4-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: 67956733 total, 39836 skipped (flags/unmapped)
Fragments: 34066930 total (33817924 tlen-paired, 2725 hash-paired, 330 singletons, 11714 discordant, 234237 orphans, 8802 too large [>5000 bp], 10785122 duplicates)
Reads: 62679776 total, 47860 skipped (flags/unmapped)
Fragments: 31423606 total (31171437 tlen-paired, 2463 hash-paired, 268 singletons, 16752 discordant, 232686 orphans, 8829 too large [>5000 bp], 10154371 duplicates)
Reads: 67288856 total, 42688 skipped (flags/unmapped)
Fragments: 33737929 total (33466194 tlen-paired, 3917 hash-paired, 252 singletons, 14364 discordant, 253202 orphans, 11882 too large [>5000 bp], 11017316 duplicates)
Reads: 73961719 total, 67261 skipped (flags/unmapped)
Fragments: 37140826 total (36554231 tlen-paired, 1286 hash-paired, 282 singletons, 109419 discordant, 475608 orphans, 44348 too large [>5000 bp], 12144767 duplicates)