Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5ZF-N1-BDNA-1_A23NMNVLT4_1/1136_5ZF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/2c6f0d7038f88191aa12b87a2479b1/.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/ae/2c6f0d7038f88191aa12b87a2479b1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_5ZF-N1-BDNA-1_A23NMNVLT4_1/1136_5ZF-N1-BDNA-1_A23NMNVLT4_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_5ZF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5ZF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5ZF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5ZF-N1-BDNA-1_A23NMNVLT4_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: 80332885 total, 59551 skipped (flags/unmapped)
Fragments: 40237915 total (40003136 tlen-paired, 3186 hash-paired, 321 singletons, 11487 discordant, 219785 orphans, 8805 too large [>5000 bp], 12635703 duplicates)
Reads: 85837337 total, 51150 skipped (flags/unmapped)
Fragments: 42995174 total (42760635 tlen-paired, 3069 hash-paired, 411 singletons, 7775 discordant, 223284 orphans, 9767 too large [>5000 bp], 13375939 duplicates)
Reads: 95263016 total, 53906 skipped (flags/unmapped)
Fragments: 47721437 total (47444420 tlen-paired, 3818 hash-paired, 308 singletons, 11329 discordant, 261562 orphans, 14053 too large [>5000 bp], 15196256 duplicates)
Reads: 95744397 total, 89795 skipped (flags/unmapped)
Fragments: 48034162 total (47388334 tlen-paired, 1874 hash-paired, 387 singletons, 122252 discordant, 521315 orphans, 53990 too large [>5000 bp], 15317038 duplicates)