Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_D6-N1-BDNA-1_A23TNVNLT4_1/1267_D6-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/3b17b372a2297c9765eedf46b0b2f5/.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/33/3b17b372a2297c9765eedf46b0b2f5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_D6-N1-BDNA-1_A23TNVNLT4_1/1267_D6-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] [W::hts_idx_load3] The index file is older than the data file: 1267_D6-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1267_D6-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_D6-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_D6-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: 90315808 total, 62598 skipped (flags/unmapped)
Fragments: 45263138 total (44955091 tlen-paired, 3493 hash-paired, 423 singletons, 13686 discordant, 290445 orphans, 8901 too large [>5000 bp], 17705627 duplicates)
Reads: 96777037 total, 54560 skipped (flags/unmapped)
Fragments: 48503565 total (48186740 tlen-paired, 4206 hash-paired, 540 singletons, 9188 discordant, 302891 orphans, 9389 too large [>5000 bp], 18671335 duplicates)
Reads: 105805080 total, 60467 skipped (flags/unmapped)
Fragments: 53026279 total (52657809 tlen-paired, 4837 hash-paired, 396 singletons, 13838 discordant, 349399 orphans, 20925 too large [>5000 bp], 20892637 duplicates)
Reads: 107121241 total, 103548 skipped (flags/unmapped)
Fragments: 53799211 total (52898261 tlen-paired, 4865 hash-paired, 480 singletons, 173946 discordant, 721659 orphans, 70705 too large [>5000 bp], 21206703 duplicates)