Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_82G-N1-BDNA-1_A23NLN3LT4_1/1136_82G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/e570086a0338beee3ed8631592af1d/.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/57/e570086a0338beee3ed8631592af1d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_82G-N1-BDNA-1_A23NLN3LT4_1/1136_82G-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] [W::hts_idx_load3] The index file is older than the data file: 1136_82G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_82G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_82G-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_82G-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: 77688466 total, 56005 skipped (flags/unmapped)
Fragments: 38941803 total (38650490 tlen-paired, 2724 hash-paired, 320 singletons, 14180 discordant, 274089 orphans, 11632 too large [>5000 bp], 13656165 duplicates)
Reads: 92685022 total, 84276 skipped (flags/unmapped)
Fragments: 46567413 total (45742365 tlen-paired, 2374 hash-paired, 352 singletons, 158666 discordant, 663656 orphans, 64964 too large [>5000 bp], 16428459 duplicates)
Reads: 84134732 total, 47951 skipped (flags/unmapped)
Fragments: 42175846 total (41876596 tlen-paired, 3172 hash-paired, 401 singletons, 9753 discordant, 285924 orphans, 10707 too large [>5000 bp], 14527981 duplicates)
Reads: 92011735 total, 52461 skipped (flags/unmapped)
Fragments: 46129251 total (45776847 tlen-paired, 3338 hash-paired, 362 singletons, 14192 discordant, 334512 orphans, 17823 too large [>5000 bp], 16278421 duplicates)