Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/0d22bbcf006372dad2cd001cedab1e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_2LI-N1-BDNA-1_2375WFLT3_s08/1029_2LI-N1-BDNA-1_2375WFLT3_s08.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/cf/0d22bbcf006372dad2cd001cedab1e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_2LI-N1-BDNA-1_2375WFLT3_s08/1029_2LI-N1-BDNA-1_2375WFLT3_s08.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_2LI-N1-BDNA-1_2375WFLT3_s08.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2LI-N1-BDNA-1_2375WFLT3_s08.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2LI-N1-BDNA-1_2375WFLT3_s08.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2LI-N1-BDNA-1_2375WFLT3_s08.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: 59640488 total, 52910 skipped (flags/unmapped)
Fragments: 29995581 total (29569460 tlen-paired, 3279 hash-paired, 1015 singletons, 10000 discordant, 411827 orphans, 4629 too large [>5000 bp], 8291509 duplicates)
Reads: 65847047 total, 50798 skipped (flags/unmapped)
Fragments: 33117172 total (32634346 tlen-paired, 3014 hash-paired, 985 singletons, 10263 discordant, 468564 orphans, 15727 too large [>5000 bp], 9050241 duplicates)
Reads: 67099751 total, 91096 skipped (flags/unmapped)
Fragments: 33975175 total (32520612 tlen-paired, 3556 hash-paired, 1051 singletons, 281802 discordant, 1168154 orphans, 113755 too large [>5000 bp], 9218423 duplicates)
Reads: 64675484 total, 46845 skipped (flags/unmapped)
Fragments: 32531391 total (32072008 tlen-paired, 2782 hash-paired, 1001 singletons, 7068 discordant, 448532 orphans, 7695 too large [>5000 bp], 8813016 duplicates)