Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/a866cdb494c551c0fd7c689f4eedec/.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/2b/a866cdb494c551c0fd7c689f4eedec/.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_OUX-N1-BDNA-1_A23TY32LT4_1/1241_OUX-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_OUX-N1-BDNA-1_A23TY32LT4_1/1241_OUX-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_OUX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_OUX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_OUX-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_OUX-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: 75242310 total, 48867 skipped (flags/unmapped)
Fragments: 37759892 total (37379691 tlen-paired, 4557 hash-paired, 290 singletons, 11815 discordant, 363539 orphans, 18744 too large [>5000 bp], 14297144 duplicates)
Reads: 69604211 total, 56068 skipped (flags/unmapped)
Fragments: 34923840 total (34588561 tlen-paired, 3957 hash-paired, 392 singletons, 13321 discordant, 317609 orphans, 9232 too large [>5000 bp], 13132565 duplicates)
Reads: 76113134 total, 45756 skipped (flags/unmapped)
Fragments: 38196243 total (37841147 tlen-paired, 2361 hash-paired, 431 singletons, 9549 discordant, 342755 orphans, 9039 too large [>5000 bp], 14146936 duplicates)
Reads: 83723937 total, 89775 skipped (flags/unmapped)
Fragments: 42142300 total (41123551 tlen-paired, 2820 hash-paired, 372 singletons, 204943 discordant, 810614 orphans, 80274 too large [>5000 bp], 15884130 duplicates)