Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_4MY-N1-BDNA-1_A23NMNVLT4_1/1136_4MY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/badda74031449821cc5a27eb6ed911/.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/a0/badda74031449821cc5a27eb6ed911/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_4MY-N1-BDNA-1_A23NMNVLT4_1/1136_4MY-N1-BDNA-1_A23NMNVLT4_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: 1136_4MY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4MY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4MY-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4MY-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: 82238069 total, 65162 skipped (flags/unmapped)
Fragments: 41192862 total (40950137 tlen-paired, 3056 hash-paired, 308 singletons, 10178 discordant, 229183 orphans, 8337 too large [>5000 bp], 12698381 duplicates)
Reads: 87399748 total, 52775 skipped (flags/unmapped)
Fragments: 43784382 total (43537854 tlen-paired, 2562 hash-paired, 373 singletons, 6803 discordant, 236790 orphans, 7686 too large [>5000 bp], 13305464 duplicates)
Reads: 97401740 total, 58196 skipped (flags/unmapped)
Fragments: 48798709 total (48491328 tlen-paired, 2982 hash-paired, 305 singletons, 9873 discordant, 294221 orphans, 20326 too large [>5000 bp], 15235307 duplicates)
Reads: 98524486 total, 98929 skipped (flags/unmapped)
Fragments: 49442638 total (48714822 tlen-paired, 3196 hash-paired, 451 singletons, 142733 discordant, 581436 orphans, 61084 too large [>5000 bp], 15435281 duplicates)