Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_C35-N1-BDNA-1_2375WFLT3_s55/1029_C35-N1-BDNA-1_2375WFLT3_s55.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/d983b3516a81cce7d38090bba38a5e/.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/a8/d983b3516a81cce7d38090bba38a5e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_C35-N1-BDNA-1_2375WFLT3_s55/1029_C35-N1-BDNA-1_2375WFLT3_s55.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_C35-N1-BDNA-1_2375WFLT3_s55.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_C35-N1-BDNA-1_2375WFLT3_s55.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_C35-N1-BDNA-1_2375WFLT3_s55.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_C35-N1-BDNA-1_2375WFLT3_s55.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: 83067039 total, 68104 skipped (flags/unmapped)
Fragments: 41742955 total (41208770 tlen-paired, 6699 hash-paired, 1235 singletons, 12749 discordant, 513502 orphans, 13881 too large [>5000 bp], 12533561 duplicates)
Reads: 82506971 total, 69828 skipped (flags/unmapped)
Fragments: 41464310 total (40940131 tlen-paired, 4010 hash-paired, 1370 singletons, 15978 discordant, 502821 orphans, 6357 too large [>5000 bp], 12567871 duplicates)
Reads: 90631090 total, 63698 skipped (flags/unmapped)
Fragments: 45547582 total (44983087 tlen-paired, 4055 hash-paired, 1425 singletons, 12148 discordant, 546867 orphans, 10260 too large [>5000 bp], 13578088 duplicates)
Reads: 93037332 total, 120967 skipped (flags/unmapped)
Fragments: 46993087 total (45329524 tlen-paired, 4027 hash-paired, 1538 singletons, 327257 discordant, 1330741 orphans, 131235 too large [>5000 bp], 14047227 duplicates)