Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/55f6f2be50be7c72ed2e86a2d62245/.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/36/55f6f2be50be7c72ed2e86a2d62245/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_02D-N1-BDNA-1_A23NLN3LT4_1/1136_02D-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_02D-N1-BDNA-1_A23NLN3LT4_1/1136_02D-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_02D-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_02D-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_02D-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_02D-N1-BDNA-1_A23NLN3LT4_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: 64636566 total, 50703 skipped (flags/unmapped)
Fragments: 32433671 total (32120103 tlen-paired, 2901 hash-paired, 261 singletons, 9386 discordant, 301020 orphans, 9901 too large [>5000 bp], 11392302 duplicates)
Reads: 69335843 total, 43632 skipped (flags/unmapped)
Fragments: 34803933 total (34436033 tlen-paired, 2426 hash-paired, 268 singletons, 8787 discordant, 356419 orphans, 20516 too large [>5000 bp], 12248543 duplicates)
Reads: 70305076 total, 42685 skipped (flags/unmapped)
Fragments: 35284073 total (34951036 tlen-paired, 2249 hash-paired, 322 singletons, 6601 discordant, 323865 orphans, 9216 too large [>5000 bp], 12061344 duplicates)
Reads: 76724147 total, 77736 skipped (flags/unmapped)
Fragments: 38642257 total (37626273 tlen-paired, 2701 hash-paired, 316 singletons, 205660 discordant, 807307 orphans, 84760 too large [>5000 bp], 13582275 duplicates)