Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/db83d87c578538593b543a48171754/.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/a8/db83d87c578538593b543a48171754/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_75S-N1-BDNA-1_B23KFG5LT4_1/1136_75S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_75S-N1-BDNA-1_B23KFG5LT4_1/1136_75S-N1-BDNA-1_B23KFG5LT4_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_75S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_75S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_75S-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_75S-N1-BDNA-1_B23KFG5LT4_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: 77904913 total, 46850 skipped (flags/unmapped)
Fragments: 39053178 total (38770992 tlen-paired, 3269 hash-paired, 307 singletons, 10528 discordant, 268082 orphans, 10048 too large [>5000 bp], 15303630 duplicates)
Reads: 71114195 total, 55464 skipped (flags/unmapped)
Fragments: 35647275 total (35376012 tlen-paired, 3464 hash-paired, 412 singletons, 14428 discordant, 252959 orphans, 8776 too large [>5000 bp], 14309534 duplicates)
Reads: 77797123 total, 48602 skipped (flags/unmapped)
Fragments: 39007258 total (38692058 tlen-paired, 2668 hash-paired, 323 singletons, 12501 discordant, 299708 orphans, 17018 too large [>5000 bp], 15763629 duplicates)
Reads: 86001048 total, 77494 skipped (flags/unmapped)
Fragments: 43199037 total (42463610 tlen-paired, 2672 hash-paired, 386 singletons, 144375 discordant, 587994 orphans, 56930 too large [>5000 bp], 17482352 duplicates)