Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/7cd93d783275e99b835f5767519ee3/.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/b8/7cd93d783275e99b835f5767519ee3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BBPA-N1-BDNA-1_B23H2GYLT3_1/1029_BBPA-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_BBPA-N1-BDNA-1_B23H2GYLT3_1/1029_BBPA-N1-BDNA-1_B23H2GYLT3_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: 1029_BBPA-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BBPA-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BBPA-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BBPA-N1-BDNA-1_B23H2GYLT3_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: 105226327 total, 90737 skipped (flags/unmapped)
Fragments: 52869410 total (52217676 tlen-paired, 14297 hash-paired, 8524 singletons, 10865 discordant, 618048 orphans, 11671 too large [>5000 bp], 12639455 duplicates)
Reads: 105984832 total, 77518 skipped (flags/unmapped)
Fragments: 53273379 total (52575268 tlen-paired, 15190 hash-paired, 8354 singletons, 10147 discordant, 664420 orphans, 16665 too large [>5000 bp], 12649117 duplicates)
Reads: 115456059 total, 81175 skipped (flags/unmapped)
Fragments: 58037013 total (57290923 tlen-paired, 13857 hash-paired, 9149 singletons, 8189 discordant, 714895 orphans, 12451 too large [>5000 bp], 13791239 duplicates)
Reads: 118772217 total, 135482 skipped (flags/unmapped)
Fragments: 60055751 total (57757838 tlen-paired, 15525 hash-paired, 9537 singletons, 456509 discordant, 1816342 orphans, 175556 too large [>5000 bp], 14092373 duplicates)