Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_4VP-N1-BDNA-1_A23NMNVLT4_1/1136_4VP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/e709d769bbf3c18795e689a086f99a/.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/35/e709d769bbf3c18795e689a086f99a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_4VP-N1-BDNA-1_A23NMNVLT4_1/1136_4VP-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_4VP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4VP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4VP-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4VP-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: 82545569 total, 63287 skipped (flags/unmapped)
Fragments: 41375235 total (41072345 tlen-paired, 2648 hash-paired, 315 singletons, 13070 discordant, 286857 orphans, 9492 too large [>5000 bp], 13631168 duplicates)
Reads: 89405322 total, 53151 skipped (flags/unmapped)
Fragments: 44818112 total (44505806 tlen-paired, 2477 hash-paired, 359 singletons, 9242 discordant, 300228 orphans, 8267 too large [>5000 bp], 14497955 duplicates)
Reads: 89579943 total, 55966 skipped (flags/unmapped)
Fragments: 44907353 total (44558969 tlen-paired, 3001 hash-paired, 275 singletons, 11912 discordant, 333196 orphans, 21371 too large [>5000 bp], 14958397 duplicates)
Reads: 98793155 total, 97997 skipped (flags/unmapped)
Fragments: 49626858 total (48747248 tlen-paired, 3244 hash-paired, 395 singletons, 174176 discordant, 701795 orphans, 71816 too large [>5000 bp], 16524779 duplicates)