Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHOU-N1-BDNA-1_B23L5TMLT4_1/1029_BHOU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/39da6a4789a5e95566e5f691dd296d/.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/91/39da6a4789a5e95566e5f691dd296d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHOU-N1-BDNA-1_B23L5TMLT4_1/1029_BHOU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> 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_BHOU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHOU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHOU-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHOU-N1-BDNA-1_B23L5TMLT4_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: 114673726 total, 84210 skipped (flags/unmapped)
Fragments: 57549617 total (56991009 tlen-paired, 5457 hash-paired, 815 singletons, 19967 discordant, 532369 orphans, 11733 too large [>5000 bp], 21276777 duplicates)
Reads: 121323357 total, 73863 skipped (flags/unmapped)
Fragments: 60884960 total (60313886 tlen-paired, 5888 hash-paired, 805 singletons, 13994 discordant, 550387 orphans, 15383 too large [>5000 bp], 22266568 duplicates)
Reads: 132649007 total, 79691 skipped (flags/unmapped)
Fragments: 66576132 total (65899603 tlen-paired, 9089 hash-paired, 634 singletons, 21234 discordant, 645572 orphans, 31629 too large [>5000 bp], 24753177 duplicates)
Reads: 133777386 total, 134489 skipped (flags/unmapped)
Fragments: 67375675 total (65649192 tlen-paired, 5255 hash-paired, 658 singletons, 334073 discordant, 1386497 orphans, 139351 too large [>5000 bp], 24995863 duplicates)