Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/a6b06afe327b0d4dfc52774d61ea73/.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/2e/a6b06afe327b0d4dfc52774d61ea73/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_HK0-N1-BDNA-1_B23KFG5LT4_1/1029_HK0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_HK0-N1-BDNA-1_B23KFG5LT4_1/1029_HK0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_HK0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_HK0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_HK0-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 1029_HK0-N1-BDNA-1_B23KFG5LT4_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: 63116752 total, 48226 skipped (flags/unmapped)
Fragments: 31643502 total (31390931 tlen-paired, 2044 hash-paired, 326 singletons, 13679 discordant, 236522 orphans, 9185 too large [>5000 bp], 12530367 duplicates)
Reads: 67377131 total, 40445 skipped (flags/unmapped)
Fragments: 33782940 total (33526878 tlen-paired, 1703 hash-paired, 362 singletons, 9549 discordant, 244448 orphans, 7808 too large [>5000 bp], 12988060 duplicates)
Reads: 67749772 total, 43876 skipped (flags/unmapped)
Fragments: 33971706 total (33680635 tlen-paired, 2347 hash-paired, 304 singletons, 11928 discordant, 276492 orphans, 19640 too large [>5000 bp], 13494557 duplicates)
Reads: 74801470 total, 69793 skipped (flags/unmapped)
Fragments: 37583777 total (36907629 tlen-paired, 2302 hash-paired, 327 singletons, 131759 discordant, 541760 orphans, 53105 too large [>5000 bp], 14943767 duplicates)