Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/8d5835922c9ceaebc5ee45d56c8040/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_GW0-N1-BDNA-1_2375WFLT3_s72/1029_GW0-N1-BDNA-1_2375WFLT3_s72.recalibrated.bam
  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/18/8d5835922c9ceaebc5ee45d56c8040/.command.run
==> 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_GW0-N1-BDNA-1_2375WFLT3_s72.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GW0-N1-BDNA-1_2375WFLT3_s72.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GW0-N1-BDNA-1_2375WFLT3_s72.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_GW0-N1-BDNA-1_2375WFLT3_s72.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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 47986249 total, 38476 skipped (flags/unmapped)
Fragments: 24137822 total (23784945 tlen-paired, 2617 hash-paired, 709 singletons, 6921 discordant, 342630 orphans, 7734 too large [>5000 bp], 6200131 duplicates)
Reads: 47544571 total, 41188 skipped (flags/unmapped)
Fragments: 23916384 total (23568212 tlen-paired, 2354 hash-paired, 766 singletons, 8419 discordant, 336633 orphans, 4007 too large [>5000 bp], 6215663 duplicates)
Reads: 52312724 total, 36545 skipped (flags/unmapped)
Fragments: 26318809 total (25936445 tlen-paired, 2415 hash-paired, 780 singletons, 6084 discordant, 373085 orphans, 6213 too large [>5000 bp], 6682175 duplicates)
Reads: 54068455 total, 68581 skipped (flags/unmapped)
Fragments: 27374153 total (26202713 tlen-paired, 2187 hash-paired, 808 singletons, 233165 discordant, 935280 orphans, 93828 too large [>5000 bp], 6969990 duplicates)