Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2QY-N1-BDNA-1_A23H3NYLT3_1/1136_2QY-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/93746988ebd62c0ece36ae3118f6d8/.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/1f/93746988ebd62c0ece36ae3118f6d8/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_2QY-N1-BDNA-1_A23H3NYLT3_1/1136_2QY-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
==> 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: 1136_2QY-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QY-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QY-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QY-N1-BDNA-1_A23H3NYLT3_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: 53800354 total, 42677 skipped (flags/unmapped)
Fragments: 27098526 total (26627755 tlen-paired, 4665 hash-paired, 4845 singletons, 4921 discordant, 456340 orphans, 10905 too large [>5000 bp], 3179655 duplicates)
Reads: 54397702 total, 50128 skipped (flags/unmapped)
Fragments: 27383701 total (26936818 tlen-paired, 5647 hash-paired, 4959 singletons, 5546 discordant, 430731 orphans, 7931 too large [>5000 bp], 3239067 duplicates)
Reads: 59861930 total, 43193 skipped (flags/unmapped)
Fragments: 30161548 total (29633070 tlen-paired, 5638 hash-paired, 5326 singletons, 4839 discordant, 512675 orphans, 6821 too large [>5000 bp], 3512252 duplicates)
Reads: 60459218 total, 75704 skipped (flags/unmapped)
Fragments: 30724802 total (29085382 tlen-paired, 4657 hash-paired, 5396 singletons, 331281 discordant, 1298086 orphans, 118696 too large [>5000 bp], 3518046 duplicates)