Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/83b9285b9808fada648dd028dd0641/.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/0d/83b9285b9808fada648dd028dd0641/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_mK-N1-BDNA-1_B23KGCJLT4_1/659_mK-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_mK-N1-BDNA-1_B23KGCJLT4_1/659_mK-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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_mK-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_mK-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_mK-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_mK-N1-BDNA-1_B23KGCJLT4_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: 97378699 total, 73353 skipped (flags/unmapped)
Fragments: 48816476 total (48433339 tlen-paired, 4760 hash-paired, 476 singletons, 23303 discordant, 354598 orphans, 13734 too large [>5000 bp], 19375975 duplicates)
Reads: 104445168 total, 66629 skipped (flags/unmapped)
Fragments: 52360291 total (51930691 tlen-paired, 4700 hash-paired, 391 singletons, 20793 discordant, 403716 orphans, 31032 too large [>5000 bp], 20915049 duplicates)
Reads: 105143257 total, 61221 skipped (flags/unmapped)
Fragments: 52706111 total (52329529 tlen-paired, 3305 hash-paired, 548 singletons, 16503 discordant, 356226 orphans, 13294 too large [>5000 bp], 20515934 duplicates)
Reads: 115329663 total, 102617 skipped (flags/unmapped)
Fragments: 57911986 total (56987593 tlen-paired, 4435 hash-paired, 430 singletons, 175568 discordant, 743960 orphans, 73732 too large [>5000 bp], 23161751 duplicates)