Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7RX-N1-BDNA-1_A23NLN3LT4_1/1136_7RX-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/febd7d4520a960481fd4def7180fb0/.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/58/febd7d4520a960481fd4def7180fb0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7RX-N1-BDNA-1_A23NLN3LT4_1/1136_7RX-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_7RX-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_7RX-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_7RX-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RX-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: 68705785 total, 46795 skipped (flags/unmapped)
Fragments: 34476039 total (34151301 tlen-paired, 2384 hash-paired, 426 singletons, 8760 discordant, 313168 orphans, 10253 too large [>5000 bp], 12145723 duplicates)
Reads: 64331872 total, 53841 skipped (flags/unmapped)
Fragments: 32279259 total (31964325 tlen-paired, 2537 hash-paired, 380 singletons, 13438 discordant, 298579 orphans, 9236 too large [>5000 bp], 11616864 duplicates)
Reads: 76008923 total, 52942 skipped (flags/unmapped)
Fragments: 38140194 total (37761355 tlen-paired, 2844 hash-paired, 297 singletons, 13094 discordant, 362604 orphans, 19247 too large [>5000 bp], 13774874 duplicates)
Reads: 76729131 total, 84683 skipped (flags/unmapped)
Fragments: 38630223 total (37673016 tlen-paired, 3569 hash-paired, 308 singletons, 187710 discordant, 765620 orphans, 74965 too large [>5000 bp], 13876284 duplicates)