Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/2f4d7ccf110094a720d83739ab1d81/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_BLBE-N1-BDNA-1_B23KGCJLT4_1/1029_BLBE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  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/6a/2f4d7ccf110094a720d83739ab1d81/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_BLBE-N1-BDNA-1_B23KGCJLT4_1/1029_BLBE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BLBE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLBE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BLBE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLBE-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: 76391141 total, 55584 skipped (flags/unmapped)
Fragments: 38289858 total (38001755 tlen-paired, 3641 hash-paired, 379 singletons, 13637 discordant, 270446 orphans, 13333 too large [>5000 bp], 15010696 duplicates)
Reads: 81500417 total, 45783 skipped (flags/unmapped)
Fragments: 40855474 total (40567083 tlen-paired, 2882 hash-paired, 366 singletons, 9629 discordant, 275514 orphans, 9783 too large [>5000 bp], 15684129 duplicates)
Reads: 89831465 total, 51165 skipped (flags/unmapped)
Fragments: 45038147 total (44680724 tlen-paired, 3410 hash-paired, 387 singletons, 14141 discordant, 339485 orphans, 21939 too large [>5000 bp], 17687371 duplicates)
Reads: 90225527 total, 78214 skipped (flags/unmapped)
Fragments: 45331525 total (44527384 tlen-paired, 3024 hash-paired, 390 singletons, 153568 discordant, 647159 orphans, 65906 too large [>5000 bp], 17836117 duplicates)