Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_OQZ-N1-BDNA-1_A23TNVNLT4_1/1241_OQZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/899f5d9f7bfa796a68b470aa455845/.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/5c/899f5d9f7bfa796a68b470aa455845/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_OQZ-N1-BDNA-1_A23TNVNLT4_1/1241_OQZ-N1-BDNA-1_A23TNVNLT4_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: 1241_OQZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_OQZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_OQZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_OQZ-N1-BDNA-1_A23TNVNLT4_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: 77822018 total, 72720 skipped (flags/unmapped)
Fragments: 39011721 total (38698188 tlen-paired, 3295 hash-paired, 424 singletons, 16748 discordant, 293066 orphans, 9673 too large [>5000 bp], 14628318 duplicates)
Reads: 83478401 total, 64148 skipped (flags/unmapped)
Fragments: 41848581 total (41528581 tlen-paired, 3144 hash-paired, 417 singletons, 11661 discordant, 304778 orphans, 11143 too large [>5000 bp], 15383804 duplicates)
Reads: 90894632 total, 70891 skipped (flags/unmapped)
Fragments: 45567064 total (45196064 tlen-paired, 4032 hash-paired, 309 singletons, 16809 discordant, 349850 orphans, 19886 too large [>5000 bp], 17140303 duplicates)
Reads: 92130942 total, 106308 skipped (flags/unmapped)
Fragments: 46290860 total (45440512 tlen-paired, 4728 hash-paired, 435 singletons, 161846 discordant, 683339 orphans, 63344 too large [>5000 bp], 17390587 duplicates)