Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_032-N1-BDNA-1_2375WFLT3_s01/1029_032-N1-BDNA-1_2375WFLT3_s01.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/b6aafda7337788c1d880daf0b86f4a/.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/7d/b6aafda7337788c1d880daf0b86f4a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_032-N1-BDNA-1_2375WFLT3_s01/1029_032-N1-BDNA-1_2375WFLT3_s01.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: 1029_032-N1-BDNA-1_2375WFLT3_s01.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_032-N1-BDNA-1_2375WFLT3_s01.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_032-N1-BDNA-1_2375WFLT3_s01.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_032-N1-BDNA-1_2375WFLT3_s01.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: 71691130 total, 61096 skipped (flags/unmapped)
Fragments: 36067906 total (35536882 tlen-paired, 3619 hash-paired, 1157 singletons, 11415 discordant, 514833 orphans, 5106 too large [>5000 bp], 10820339 duplicates)
Reads: 79137654 total, 61647 skipped (flags/unmapped)
Fragments: 39812382 total (39209020 tlen-paired, 4611 hash-paired, 1235 singletons, 11164 discordant, 586352 orphans, 19415 too large [>5000 bp], 11822524 duplicates)
Reads: 81100631 total, 103466 skipped (flags/unmapped)
Fragments: 41093366 total (39252089 tlen-paired, 2966 hash-paired, 1287 singletons, 358152 discordant, 1478872 orphans, 145296 too large [>5000 bp], 12087115 duplicates)
Reads: 77038663 total, 54535 skipped (flags/unmapped)
Fragments: 38762884 total (38192098 tlen-paired, 3081 hash-paired, 1238 singletons, 7861 discordant, 558606 orphans, 9102 too large [>5000 bp], 11430803 duplicates)