Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BQMQ-N1-BDNA-1_235YY7LT3_1/1029_BQMQ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BQMQ-N1-BDNA-1_235YY7LT3_1/1029_BQMQ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/eaab78ee36536ba4a35145dc1b87c7/.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/9f/eaab78ee36536ba4a35145dc1b87c7/.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_BQMQ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQMQ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQMQ-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQMQ-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 46944450 total, 42687 skipped (flags/unmapped)
Fragments: 23720466 total (23167010 tlen-paired, 2651 hash-paired, 2716 singletons, 5256 discordant, 542833 orphans, 3190 too large [>5000 bp], 6157145 duplicates)
Reads: 50328489 total, 42500 skipped (flags/unmapped)
Fragments: 25437409 total (24830557 tlen-paired, 2133 hash-paired, 2836 singletons, 3814 discordant, 598069 orphans, 6038 too large [>5000 bp], 6434920 duplicates)
Reads: 51997558 total, 44084 skipped (flags/unmapped)
Fragments: 26278023 total (25642284 tlen-paired, 2475 hash-paired, 2793 singletons, 5826 discordant, 624645 orphans, 12433 too large [>5000 bp], 6709061 duplicates)
Reads: 54181511 total, 68979 skipped (flags/unmapped)
Fragments: 27728843 total (25635336 tlen-paired, 1979 hash-paired, 2963 singletons, 413644 discordant, 1674921 orphans, 166365 too large [>5000 bp], 6861454 duplicates)