Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/56d1aef3e7eab8dd89f2de33ed228b/.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/04/56d1aef3e7eab8dd89f2de33ed228b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_YES-N1-BDNA-1_A23NLN3LT4_1/1029_YES-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/1029_YES-N1-BDNA-1_A23NLN3LT4_1/1029_YES-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: 1029_YES-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_YES-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1029_YES-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_YES-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: 79160324 total, 78567 skipped (flags/unmapped)
Fragments: 39715820 total (39314733 tlen-paired, 4555 hash-paired, 328 singletons, 22385 discordant, 373819 orphans, 12132 too large [>5000 bp], 14215658 duplicates)
Reads: 85670951 total, 66056 skipped (flags/unmapped)
Fragments: 42985182 total (42574374 tlen-paired, 3994 hash-paired, 471 singletons, 16359 discordant, 389984 orphans, 12493 too large [>5000 bp], 15135656 duplicates)
Reads: 85087553 total, 71161 skipped (flags/unmapped)
Fragments: 42695772 total (42264352 tlen-paired, 4863 hash-paired, 291 singletons, 18769 discordant, 407497 orphans, 16318 too large [>5000 bp], 15452172 duplicates)
Reads: 94137306 total, 115268 skipped (flags/unmapped)
Fragments: 47352487 total (46293418 tlen-paired, 3476 hash-paired, 382 singletons, 205631 discordant, 849580 orphans, 83513 too large [>5000 bp], 17109467 duplicates)