Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/a6fdf139cb30032428c8bc2964db47/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_GLM-N1-BDNA-1_A23NLN3LT4_1/1029_GLM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  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/f4/a6fdf139cb30032428c8bc2964db47/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_GLM-N1-BDNA-1_A23NLN3LT4_1/1029_GLM-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: 1029_GLM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GLM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GLM-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GLM-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: 77761319 total, 49775 skipped (flags/unmapped)
Fragments: 38989046 total (38658242 tlen-paired, 5134 hash-paired, 306 singletons, 14072 discordant, 311292 orphans, 22525 too large [>5000 bp], 14121107 duplicates)
Reads: 72611361 total, 58855 skipped (flags/unmapped)
Fragments: 36397354 total (36109554 tlen-paired, 3581 hash-paired, 295 singletons, 15715 discordant, 268209 orphans, 13151 too large [>5000 bp], 13083416 duplicates)
Reads: 78595895 total, 46377 skipped (flags/unmapped)
Fragments: 39402887 total (39112311 tlen-paired, 2687 hash-paired, 367 singletons, 10671 discordant, 276851 orphans, 10481 too large [>5000 bp], 13859763 duplicates)
Reads: 85790949 total, 84614 skipped (flags/unmapped)
Fragments: 43096112 total (42336940 tlen-paired, 2519 hash-paired, 314 singletons, 146454 discordant, 609885 orphans, 62155 too large [>5000 bp], 15606378 duplicates)