Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/336e55a6108e16340ade24cbdf5436/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/336e55a6108e16340ade24cbdf5436/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BF2U-N1-BDNA-1_235YY7LT3_1/1029_BF2U-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_BF2U-N1-BDNA-1_235YY7LT3_1/1029_BF2U-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
==> 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_BF2U-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BF2U-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BF2U-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BF2U-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: 52437843 total, 35357 skipped (flags/unmapped)
Fragments: 26315824 total (26066313 tlen-paired, 2647 hash-paired, 2527 singletons, 5552 discordant, 238785 orphans, 6075 too large [>5000 bp], 5388815 duplicates)
Reads: 48339939 total, 38747 skipped (flags/unmapped)
Fragments: 24260965 total (24022779 tlen-paired, 2801 hash-paired, 2526 singletons, 7835 discordant, 225024 orphans, 3406 too large [>5000 bp], 5081643 duplicates)
Reads: 53638670 total, 50094 skipped (flags/unmapped)
Fragments: 27026078 total (26305626 tlen-paired, 2257 hash-paired, 2684 singletons, 138443 discordant, 577068 orphans, 58086 too large [>5000 bp], 5588328 duplicates)
Reads: 48403235 total, 37387 skipped (flags/unmapped)
Fragments: 24292238 total (24053979 tlen-paired, 2893 hash-paired, 2421 singletons, 6430 discordant, 226515 orphans, 5154 too large [>5000 bp], 5027251 duplicates)