Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/e07b8cd865bda8eacd98fdeab76c7f/.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/bd/e07b8cd865bda8eacd98fdeab76c7f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_002-N1-BDNA-1_A23KFG7LT4_1/1136_002-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_002-N1-BDNA-1_A23KFG7LT4_1/1136_002-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_002-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_002-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_002-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_002-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: 69080278 total, 44211 skipped (flags/unmapped)
Fragments: 34622046 total (34388037 tlen-paired, 2211 hash-paired, 304 singletons, 10117 discordant, 221377 orphans, 6828 too large [>5000 bp], 11218142 duplicates)
Reads: 73958958 total, 40459 skipped (flags/unmapped)
Fragments: 37066262 total (36825215 tlen-paired, 2443 hash-paired, 427 singletons, 7145 discordant, 231032 orphans, 8717 too large [>5000 bp], 11672119 duplicates)
Reads: 81345944 total, 67149 skipped (flags/unmapped)
Fragments: 40858290 total (40178046 tlen-paired, 2197 hash-paired, 327 singletons, 131140 discordant, 546580 orphans, 54561 too large [>5000 bp], 13260847 duplicates)
Reads: 80269871 total, 43161 skipped (flags/unmapped)
Fragments: 40230404 total (39951504 tlen-paired, 3979 hash-paired, 234 singletons, 10315 discordant, 264372 orphans, 15254 too large [>5000 bp], 13036237 duplicates)