Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_5KM-N1-BDNA-1_A23NLN3LT4_1/1136_5KM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/24ffb7658b516dfdd023b8eaca3446/.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/18/24ffb7658b516dfdd023b8eaca3446/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_5KM-N1-BDNA-1_A23NLN3LT4_1/1136_5KM-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_5KM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5KM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_5KM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5KM-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: 81161139 total, 60538 skipped (flags/unmapped)
Fragments: 40680536 total (40376172 tlen-paired, 2446 hash-paired, 404 singletons, 18043 discordant, 283471 orphans, 11702 too large [>5000 bp], 14621692 duplicates)
Reads: 86740661 total, 50324 skipped (flags/unmapped)
Fragments: 43476674 total (43175449 tlen-paired, 3625 hash-paired, 366 singletons, 12313 discordant, 284921 orphans, 11138 too large [>5000 bp], 15422178 duplicates)
Reads: 95712549 total, 85932 skipped (flags/unmapped)
Fragments: 48062788 total (47296689 tlen-paired, 3527 hash-paired, 329 singletons, 142615 discordant, 619628 orphans, 60499 too large [>5000 bp], 17447996 duplicates)
Reads: 95484522 total, 56583 skipped (flags/unmapped)
Fragments: 47860708 total (47498567 tlen-paired, 3359 hash-paired, 292 singletons, 18153 discordant, 340337 orphans, 23576 too large [>5000 bp], 17338768 duplicates)