Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/887d93493bcc2c44d95ae6a0d73661/.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/85/887d93493bcc2c44d95ae6a0d73661/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_17K-N1-BDNA-1_A23NLN3LT4_1/1136_17K-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_17K-N1-BDNA-1_A23NLN3LT4_1/1136_17K-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_17K-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_17K-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_17K-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_17K-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: 82194165 total, 56536 skipped (flags/unmapped)
Fragments: 41179936 total (40917209 tlen-paired, 3678 hash-paired, 286 singletons, 16136 discordant, 242627 orphans, 10335 too large [>5000 bp], 13480053 duplicates)
Reads: 88833996 total, 45879 skipped (flags/unmapped)
Fragments: 44507594 total (44246644 tlen-paired, 3625 hash-paired, 453 singletons, 11828 discordant, 245044 orphans, 9213 too large [>5000 bp], 14297730 duplicates)
Reads: 87862546 total, 51317 skipped (flags/unmapped)
Fragments: 44024850 total (43724390 tlen-paired, 5412 hash-paired, 338 singletons, 14595 discordant, 280115 orphans, 20991 too large [>5000 bp], 14500382 duplicates)
Reads: 97001787 total, 80637 skipped (flags/unmapped)
Fragments: 48665598 total (48039815 tlen-paired, 2223 hash-paired, 361 singletons, 118538 discordant, 504661 orphans, 47488 too large [>5000 bp], 16072438 duplicates)