Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_63V-N1-BDNA-1_B23KGCJLT4_1/1136_63V-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/5a0412d69555ad17fdba50553acd20/.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/47/5a0412d69555ad17fdba50553acd20/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_63V-N1-BDNA-1_B23KGCJLT4_1/1136_63V-N1-BDNA-1_B23KGCJLT4_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: 1136_63V-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_63V-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_63V-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_63V-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: 99965033 total, 67023 skipped (flags/unmapped)
Fragments: 50085275 total (49769469 tlen-paired, 3237 hash-paired, 445 singletons, 19997 discordant, 292127 orphans, 10016 too large [>5000 bp], 19979109 duplicates)
Reads: 106663266 total, 54857 skipped (flags/unmapped)
Fragments: 53438042 total (53129802 tlen-paired, 2672 hash-paired, 479 singletons, 13637 discordant, 291452 orphans, 12128 too large [>5000 bp], 21050037 duplicates)
Reads: 117533092 total, 93810 skipped (flags/unmapped)
Fragments: 58966602 total (58215605 tlen-paired, 2719 hash-paired, 442 singletons, 136966 discordant, 610870 orphans, 58695 too large [>5000 bp], 23759234 duplicates)
Reads: 116946427 total, 62599 skipped (flags/unmapped)
Fragments: 58600023 total (58224367 tlen-paired, 4545 hash-paired, 418 singletons, 19687 discordant, 351006 orphans, 17603 too large [>5000 bp], 23556665 duplicates)