Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_6BY-N1-BDNA-1_A23TY32LT4_1/1241_6BY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/ac394f238e9c71d605d843aa50525b/.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/60/ac394f238e9c71d605d843aa50525b/.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_6BY-N1-BDNA-1_A23TY32LT4_1/1241_6BY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_6BY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_6BY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_6BY-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_6BY-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: 64120210 total, 51458 skipped (flags/unmapped)
Fragments: 32205782 total (31833165 tlen-paired, 3032 hash-paired, 295 singletons, 10517 discordant, 358773 orphans, 8128 too large [>5000 bp], 12830765 duplicates)
Reads: 75899412 total, 48214 skipped (flags/unmapped)
Fragments: 38129526 total (37667149 tlen-paired, 2843 hash-paired, 298 singletons, 10670 discordant, 448566 orphans, 20505 too large [>5000 bp], 15229438 duplicates)
Reads: 69089552 total, 44700 skipped (flags/unmapped)
Fragments: 34710202 total (34309350 tlen-paired, 2777 hash-paired, 357 singletons, 7257 discordant, 390461 orphans, 7633 too large [>5000 bp], 13601373 duplicates)
Reads: 77228529 total, 84107 skipped (flags/unmapped)
Fragments: 38979454 total (37706872 tlen-paired, 3176 hash-paired, 326 singletons, 254034 discordant, 1015046 orphans, 100443 too large [>5000 bp], 15443217 duplicates)