Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_IKL-N1-BDNA-1_B23KGCJLT4_1/1029_IKL-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/8ddaca505056c8799800c6d3586d33/.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/1b/8ddaca505056c8799800c6d3586d33/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_IKL-N1-BDNA-1_B23KGCJLT4_1/1029_IKL-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] The index file is older than the data file: 1029_IKL-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_IKL-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_IKL-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_IKL-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: 76099561 total, 56162 skipped (flags/unmapped)
Fragments: 38151624 total (37852917 tlen-paired, 3429 hash-paired, 404 singletons, 12057 discordant, 282817 orphans, 11686 too large [>5000 bp], 15897510 duplicates)
Reads: 80781060 total, 45809 skipped (flags/unmapped)
Fragments: 40507076 total (40200174 tlen-paired, 2344 hash-paired, 450 singletons, 8113 discordant, 295995 orphans, 8772 too large [>5000 bp], 16497162 duplicates)
Reads: 89492561 total, 52222 skipped (flags/unmapped)
Fragments: 44878196 total (44525783 tlen-paired, 3550 hash-paired, 370 singletons, 11382 discordant, 337111 orphans, 10714 too large [>5000 bp], 18729674 duplicates)
Reads: 89563463 total, 84406 skipped (flags/unmapped)
Fragments: 45031723 total (44122558 tlen-paired, 2239 hash-paired, 405 singletons, 174879 discordant, 731642 orphans, 73829 too large [>5000 bp], 18735591 duplicates)