Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/3e5a31267857712ba4d6a29e992c47/.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/34/3e5a31267857712ba4d6a29e992c47/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_08G-N1-BDNA-1_A23KFG7LT4_1/1136_08G-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_08G-N1-BDNA-1_A23KFG7LT4_1/1136_08G-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_08G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_08G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_08G-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_08G-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: 87125970 total, 46488 skipped (flags/unmapped)
Fragments: 43645682 total (43401685 tlen-paired, 3595 hash-paired, 473 singletons, 9286 discordant, 230643 orphans, 9617 too large [>5000 bp], 14701454 duplicates)
Reads: 82180613 total, 55229 skipped (flags/unmapped)
Fragments: 41168219 total (40920697 tlen-paired, 3533 hash-paired, 347 singletons, 13505 discordant, 230137 orphans, 9715 too large [>5000 bp], 14206403 duplicates)
Reads: 95345078 total, 50206 skipped (flags/unmapped)
Fragments: 47770054 total (47459002 tlen-paired, 5247 hash-paired, 382 singletons, 14257 discordant, 291166 orphans, 23156 too large [>5000 bp], 16528454 duplicates)
Reads: 96229169 total, 81728 skipped (flags/unmapped)
Fragments: 48278900 total (47639721 tlen-paired, 3813 hash-paired, 389 singletons, 120425 discordant, 514552 orphans, 52291 too large [>5000 bp], 16758346 duplicates)