Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_H0A-N1-BDNA-1_2375WFLT3_s74/1029_H0A-N1-BDNA-1_2375WFLT3_s74.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_H0A-N1-BDNA-1_2375WFLT3_s74/1029_H0A-N1-BDNA-1_2375WFLT3_s74.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/85a09c2f20632778c32e2d8d5ea585/.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/d3/85a09c2f20632778c32e2d8d5ea585/.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: 1029_H0A-N1-BDNA-1_2375WFLT3_s74.recalibrated.bam.baiThe index file is older than the data file: 1029_H0A-N1-BDNA-1_2375WFLT3_s74.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_H0A-N1-BDNA-1_2375WFLT3_s74.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H0A-N1-BDNA-1_2375WFLT3_s74.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: 72758783 total, 65232 skipped (flags/unmapped)
Fragments: 36537037 total (36128023 tlen-paired, 3802 hash-paired, 1149 singletons, 12743 discordant, 391320 orphans, 5973 too large [>5000 bp], 11000953 duplicates)
Reads: 77885907 total, 58853 skipped (flags/unmapped)
Fragments: 39114629 total (38681467 tlen-paired, 3747 hash-paired, 1238 singletons, 8963 discordant, 419214 orphans, 9124 too large [>5000 bp], 11642223 duplicates)
Reads: 79918399 total, 62439 skipped (flags/unmapped)
Fragments: 40131782 total (39674150 tlen-paired, 4970 hash-paired, 1178 singletons, 12286 discordant, 439198 orphans, 16386 too large [>5000 bp], 11954861 duplicates)
Reads: 81360313 total, 107829 skipped (flags/unmapped)
Fragments: 41050680 total (39751385 tlen-paired, 2995 hash-paired, 1302 singletons, 248600 discordant, 1046398 orphans, 99412 too large [>5000 bp], 12187346 duplicates)