Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7RL-N1-BDNA-1_A23NLN3LT4_1/1136_7RL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/0aad6daea9c3e82e61485f476f8b07/.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/10/0aad6daea9c3e82e61485f476f8b07/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7RL-N1-BDNA-1_A23NLN3LT4_1/1136_7RL-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_7RL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_7RL-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7RL-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: 81471727 total, 61721 skipped (flags/unmapped)
Fragments: 40838449 total (40527942 tlen-paired, 4291 hash-paired, 390 singletons, 17258 discordant, 288568 orphans, 11033 too large [>5000 bp], 13674834 duplicates)
Reads: 87191265 total, 54926 skipped (flags/unmapped)
Fragments: 43712501 total (43355905 tlen-paired, 5225 hash-paired, 341 singletons, 14794 discordant, 336236 orphans, 23957 too large [>5000 bp], 14737930 duplicates)
Reads: 88067530 total, 48615 skipped (flags/unmapped)
Fragments: 44148967 total (43835695 tlen-paired, 3133 hash-paired, 415 singletons, 11600 discordant, 298124 orphans, 9760 too large [>5000 bp], 14439370 duplicates)
Reads: 96265400 total, 88093 skipped (flags/unmapped)
Fragments: 48348608 total (47539183 tlen-paired, 3462 hash-paired, 357 singletons, 156028 discordant, 649578 orphans, 65013 too large [>5000 bp], 16326477 duplicates)