Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_64R-N1-BDNA-1_A23NMNVLT4_1/1136_64R-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_64R-N1-BDNA-1_A23NMNVLT4_1/1136_64R-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/8b152db137da97afb788b1e2551cd2/.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/01/8b152db137da97afb788b1e2551cd2/.command.run
==> 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_64R-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_64R-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_64R-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_64R-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: 42504676 total, 36970 skipped (flags/unmapped)
Fragments: 21345666 total (21105203 tlen-paired, 2367 hash-paired, 178 singletons, 4816 discordant, 233102 orphans, 4827 too large [>5000 bp], 5873844 duplicates)
Reads: 45892803 total, 31911 skipped (flags/unmapped)
Fragments: 23050403 total (22794860 tlen-paired, 1987 hash-paired, 230 singletons, 3340 discordant, 249986 orphans, 5151 too large [>5000 bp], 6157533 duplicates)
Reads: 50246078 total, 34213 skipped (flags/unmapped)
Fragments: 25241609 total (24937715 tlen-paired, 2637 hash-paired, 170 singletons, 5032 discordant, 296055 orphans, 12436 too large [>5000 bp], 6972007 duplicates)
Reads: 51278016 total, 44071 skipped (flags/unmapped)
Fragments: 25889964 total (25028152 tlen-paired, 1958 hash-paired, 274 singletons, 171915 discordant, 687665 orphans, 70978 too large [>5000 bp], 7095864 duplicates)