Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_EH-N1-BDNA-1_A23TNVNLT4_1/1267_EH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/cb56a4ff597d5c9d605d653a70f6a6/.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/4d/cb56a4ff597d5c9d605d653a70f6a6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_EH-N1-BDNA-1_A23TNVNLT4_1/1267_EH-N1-BDNA-1_A23TNVNLT4_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: 1267_EH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_EH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_EH-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_EH-N1-BDNA-1_A23TNVNLT4_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: 81172564 total, 59456 skipped (flags/unmapped)
Fragments: 40699178 total (40373779 tlen-paired, 4759 hash-paired, 476 singletons, 15740 discordant, 304424 orphans, 9826 too large [>5000 bp], 14859663 duplicates)
Reads: 87335471 total, 48635 skipped (flags/unmapped)
Fragments: 43793916 total (43460365 tlen-paired, 2335 hash-paired, 485 singletons, 10930 discordant, 319801 orphans, 9645 too large [>5000 bp], 15698174 duplicates)
Reads: 96531692 total, 93584 skipped (flags/unmapped)
Fragments: 48520366 total (47595363 tlen-paired, 2860 hash-paired, 438 singletons, 177873 discordant, 743832 orphans, 70823 too large [>5000 bp], 17783489 duplicates)
Reads: 95227582 total, 54033 skipped (flags/unmapped)
Fragments: 47753889 total (47361509 tlen-paired, 6189 hash-paired, 335 singletons, 16266 discordant, 369590 orphans, 17848 too large [>5000 bp], 17494934 duplicates)