Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/6c53bf534bee71174fc917cb043881/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1047_5-N1-BDNA-1_B23KGCJLT4_1/1047_5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  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/b8/6c53bf534bee71174fc917cb043881/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1047_5-N1-BDNA-1_B23KGCJLT4_1/1047_5-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: 1047_5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_5-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1047_5-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: 79895163 total, 45719 skipped (flags/unmapped)
Fragments: 40044326 total (39773884 tlen-paired, 3047 hash-paired, 448 singletons, 10303 discordant, 256644 orphans, 8942 too large [>5000 bp], 15536385 duplicates)
Reads: 74956054 total, 54294 skipped (flags/unmapped)
Fragments: 37567489 total (37297454 tlen-paired, 3499 hash-paired, 345 singletons, 14678 discordant, 251513 orphans, 9320 too large [>5000 bp], 14825399 duplicates)
Reads: 88279646 total, 79529 skipped (flags/unmapped)
Fragments: 44331171 total (43621717 tlen-paired, 3124 hash-paired, 342 singletons, 133705 discordant, 572283 orphans, 55200 too large [>5000 bp], 17579078 duplicates)
Reads: 87952751 total, 51523 skipped (flags/unmapped)
Fragments: 44085669 total (43746268 tlen-paired, 4688 hash-paired, 361 singletons, 15153 discordant, 319199 orphans, 24725 too large [>5000 bp], 17442545 duplicates)