Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/9a40caf208c0893e4e51ebf47b2003/.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/56/9a40caf208c0893e4e51ebf47b2003/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_RON-N1-BDNA-1_A23TY32LT4_1/1241_RON-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_RON-N1-BDNA-1_A23TY32LT4_1/1241_RON-N1-BDNA-1_A23TY32LT4_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: 1241_RON-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_RON-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_RON-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_RON-N1-BDNA-1_A23TY32LT4_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: 73470437 total, 52629 skipped (flags/unmapped)
Fragments: 36834387 total (36549372 tlen-paired, 4098 hash-paired, 379 singletons, 11427 discordant, 269111 orphans, 9262 too large [>5000 bp], 14345783 duplicates)
Reads: 86449052 total, 47451 skipped (flags/unmapped)
Fragments: 43345765 total (42995470 tlen-paired, 3589 hash-paired, 260 singletons, 11773 discordant, 334673 orphans, 22502 too large [>5000 bp], 16965455 duplicates)
Reads: 78881348 total, 45083 skipped (flags/unmapped)
Fragments: 39550532 total (39257612 tlen-paired, 3078 hash-paired, 364 singletons, 7739 discordant, 281739 orphans, 8652 too large [>5000 bp], 15146190 duplicates)
Reads: 87316016 total, 86583 skipped (flags/unmapped)
Fragments: 43890409 total (43032501 tlen-paired, 3895 hash-paired, 304 singletons, 166100 discordant, 687609 orphans, 68264 too large [>5000 bp], 17160724 duplicates)