Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7YE-N1-BDNA-1_A23NLN3LT4_1/1136_7YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_7YE-N1-BDNA-1_A23NLN3LT4_1/1136_7YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/0bbdfa4210564a29e143e63b1e9c6f/.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/0d/0bbdfa4210564a29e143e63b1e9c6f/.command.run
==> 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_7YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_7YE-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7YE-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: 78814672 total, 55422 skipped (flags/unmapped)
Fragments: 39516184 total (39205408 tlen-paired, 2691 hash-paired, 330 singletons, 13977 discordant, 293778 orphans, 10495 too large [>5000 bp], 14141672 duplicates)
Reads: 84457100 total, 46853 skipped (flags/unmapped)
Fragments: 42350817 total (42028014 tlen-paired, 2158 hash-paired, 464 singletons, 9068 discordant, 311113 orphans, 10095 too large [>5000 bp], 14859687 duplicates)
Reads: 93656807 total, 88138 skipped (flags/unmapped)
Fragments: 47080996 total (46163417 tlen-paired, 2311 hash-paired, 367 singletons, 176129 discordant, 738772 orphans, 72908 too large [>5000 bp], 16927380 duplicates)
Reads: 93151636 total, 54077 skipped (flags/unmapped)
Fragments: 46707217 total (46331260 tlen-paired, 7376 hash-paired, 337 singletons, 13954 discordant, 354290 orphans, 18876 too large [>5000 bp], 16794843 duplicates)