Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_57T-N1-BDNA-1_A23NLN3LT4_1/1136_57T-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_57T-N1-BDNA-1_A23NLN3LT4_1/1136_57T-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/c7e81dd430d85c2ce5d698d40ef6bc/.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/4e/c7e81dd430d85c2ce5d698d40ef6bc/.command.run
==> 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_57T-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_57T-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1136_57T-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_57T-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: 64109019 total, 47833 skipped (flags/unmapped)
Fragments: 32143445 total (31884227 tlen-paired, 3234 hash-paired, 308 singletons, 10876 discordant, 244800 orphans, 9702 too large [>5000 bp], 11361772 duplicates)
Reads: 68775236 total, 39847 skipped (flags/unmapped)
Fragments: 34493038 total (34206085 tlen-paired, 3975 hash-paired, 260 singletons, 9369 discordant, 273349 orphans, 11461 too large [>5000 bp], 12243189 duplicates)
Reads: 69102827 total, 37765 skipped (flags/unmapped)
Fragments: 34654970 total (34385294 tlen-paired, 2105 hash-paired, 359 singletons, 7831 discordant, 259381 orphans, 7431 too large [>5000 bp], 11954749 duplicates)
Reads: 75886882 total, 64970 skipped (flags/unmapped)
Fragments: 38155120 total (37387432 tlen-paired, 2518 hash-paired, 282 singletons, 152880 discordant, 612008 orphans, 61981 too large [>5000 bp], 13557823 duplicates)