Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_3HI-N1-BDNA-1_A23TY7KLT4_1/1241_3HI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/f2c1900c9deb150db8044fa2db4789/.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/c9/f2c1900c9deb150db8044fa2db4789/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_3HI-N1-BDNA-1_A23TY7KLT4_1/1241_3HI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
==> 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: 1241_3HI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3HI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3HI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3HI-N1-BDNA-1_A23TY7KLT4_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: 75972245 total, 57750 skipped (flags/unmapped)
Fragments: 38054825 total (37829353 tlen-paired, 3061 hash-paired, 303 singletons, 10608 discordant, 211500 orphans, 8324 too large [>5000 bp], 13313593 duplicates)
Reads: 81727264 total, 46983 skipped (flags/unmapped)
Fragments: 40940636 total (40710919 tlen-paired, 2287 hash-paired, 311 singletons, 7425 discordant, 219694 orphans, 9507 too large [>5000 bp], 14041457 duplicates)
Reads: 80828461 total, 50287 skipped (flags/unmapped)
Fragments: 40491770 total (40228158 tlen-paired, 5690 hash-paired, 283 singletons, 9652 discordant, 247987 orphans, 21452 too large [>5000 bp], 14231921 duplicates)
Reads: 88877147 total, 83243 skipped (flags/unmapped)
Fragments: 44594457 total (43974715 tlen-paired, 3081 hash-paired, 343 singletons, 120129 discordant, 496189 orphans, 50761 too large [>5000 bp], 15700955 duplicates)