Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_ddF-N1-BDNA-1_A23TNVNLT4_1/659_ddF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/738c04a43c459da5561707d81671cf/.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/7e/738c04a43c459da5561707d81671cf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_ddF-N1-BDNA-1_A23TNVNLT4_1/659_ddF-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: 659_ddF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_ddF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ddF-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ddF-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: 93353570 total, 63096 skipped (flags/unmapped)
Fragments: 46805373 total (46444826 tlen-paired, 4205 hash-paired, 453 singletons, 16432 discordant, 339457 orphans, 9819 too large [>5000 bp], 16586047 duplicates)
Reads: 99820768 total, 52758 skipped (flags/unmapped)
Fragments: 50049535 total (49681862 tlen-paired, 3230 hash-paired, 553 singletons, 10931 discordant, 352959 orphans, 11226 too large [>5000 bp], 17519917 duplicates)
Reads: 109582729 total, 56580 skipped (flags/unmapped)
Fragments: 54949914 total (54510749 tlen-paired, 3923 hash-paired, 413 singletons, 16135 discordant, 418694 orphans, 22714 too large [>5000 bp], 19718455 duplicates)
Reads: 111581132 total, 94720 skipped (flags/unmapped)
Fragments: 56085403 total (55029233 tlen-paired, 3183 hash-paired, 507 singletons, 204465 discordant, 848015 orphans, 82064 too large [>5000 bp], 20131466 duplicates)