Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_BIHC-N1-BDNA-1_235YY7LT3_1/1029_BIHC-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_BIHC-N1-BDNA-1_235YY7LT3_1/1029_BIHC-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/5e5ff6ee7ca01a6c74625bf1893557/.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/c0/5e5ff6ee7ca01a6c74625bf1893557/.command.run
==> 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_BIHC-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_BIHC-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BIHC-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BIHC-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: 70614389 total, 57031 skipped (flags/unmapped)
Fragments: 35444052 total (35088034 tlen-paired, 2842 hash-paired, 4420 singletons, 11984 discordant, 336772 orphans, 5223 too large [>5000 bp], 8623541 duplicates)
Reads: 70877704 total, 54289 skipped (flags/unmapped)
Fragments: 35573640 total (35213174 tlen-paired, 3236 hash-paired, 4211 singletons, 9637 discordant, 343382 orphans, 11864 too large [>5000 bp], 8558073 duplicates)
Reads: 76776874 total, 52664 skipped (flags/unmapped)
Fragments: 38535807 total (38155716 tlen-paired, 4066 hash-paired, 4660 singletons, 8815 discordant, 362550 orphans, 9903 too large [>5000 bp], 9167695 duplicates)
Reads: 78488163 total, 81257 skipped (flags/unmapped)
Fragments: 39551514 total (38472344 tlen-paired, 3107 hash-paired, 4866 singletons, 206397 discordant, 864800 orphans, 86772 too large [>5000 bp], 9495728 duplicates)