Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/6ba8c4fd9a49d9c1c75486ee3fb4a2/.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/59/6ba8c4fd9a49d9c1c75486ee3fb4a2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3CM-N1-BDNA-1_A23KFG7LT4_1/1136_3CM-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3CM-N1-BDNA-1_A23KFG7LT4_1/1136_3CM-N1-BDNA-1_A23KFG7LT4_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: 1136_3CM-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3CM-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_3CM-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_3CM-N1-BDNA-1_A23KFG7LT4_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: 93543560 total, 53393 skipped (flags/unmapped)
Fragments: 46985838 total (46468255 tlen-paired, 2565 hash-paired, 557 singletons, 11505 discordant, 502956 orphans, 11002 too large [>5000 bp], 17815376 duplicates)
Reads: 87988621 total, 60059 skipped (flags/unmapped)
Fragments: 44191590 total (43692054 tlen-paired, 3461 hash-paired, 503 singletons, 16265 discordant, 479307 orphans, 12596 too large [>5000 bp], 17215858 duplicates)
Reads: 93156536 total, 55869 skipped (flags/unmapped)
Fragments: 46793878 total (46242936 tlen-paired, 4596 hash-paired, 423 singletons, 13669 discordant, 532254 orphans, 22794 too large [>5000 bp], 18262350 duplicates)
Reads: 103818179 total, 88075 skipped (flags/unmapped)
Fragments: 52363871 total (50790772 tlen-paired, 3761 hash-paired, 551 singletons, 314584 discordant, 1254203 orphans, 128558 too large [>5000 bp], 20370364 duplicates)