Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_1H5-N1-BDNA-1_235YY7LT3_1/1029_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_1H5-N1-BDNA-1_235YY7LT3_1/1029_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/7a07e4f4c71e04bddb5313700d9a47/.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/b3/7a07e4f4c71e04bddb5313700d9a47/.command.run
==> 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_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1H5-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1H5-N1-BDNA-1_235YY7LT3_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: 74645614 total, 68721 skipped (flags/unmapped)
Fragments: 37421553 total (37125831 tlen-paired, 7425 hash-paired, 4744 singletons, 11424 discordant, 272129 orphans, 5330 too large [>5000 bp], 8541904 duplicates)
Reads: 74930921 total, 62395 skipped (flags/unmapped)
Fragments: 37563281 total (37261577 tlen-paired, 10036 hash-paired, 4563 singletons, 9000 discordant, 278105 orphans, 12316 too large [>5000 bp], 8480598 duplicates)
Reads: 82788473 total, 88245 skipped (flags/unmapped)
Fragments: 41620057 total (40779544 tlen-paired, 5291 hash-paired, 5181 singletons, 159994 discordant, 670047 orphans, 67671 too large [>5000 bp], 9415235 duplicates)
Reads: 81307050 total, 58459 skipped (flags/unmapped)
Fragments: 40761198 total (40454468 tlen-paired, 6402 hash-paired, 5027 singletons, 8115 discordant, 287186 orphans, 9204 too large [>5000 bp], 9144448 duplicates)