Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/cd1edf8cbcf803ff380b327ee2e847/.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/75/cd1edf8cbcf803ff380b327ee2e847/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_R9T-N1-BDNA-1_A23TNVNLT4_1/1241_R9T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_R9T-N1-BDNA-1_A23TNVNLT4_1/1241_R9T-N1-BDNA-1_A23TNVNLT4_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: 1241_R9T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R9T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R9T-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_R9T-N1-BDNA-1_A23TNVNLT4_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: 111680317 total, 72084 skipped (flags/unmapped)
Fragments: 55968649 total (55590306 tlen-paired, 4967 hash-paired, 465 singletons, 18469 discordant, 354442 orphans, 12921 too large [>5000 bp], 20654788 duplicates)
Reads: 120859377 total, 59016 skipped (flags/unmapped)
Fragments: 60572441 total (60190378 tlen-paired, 3362 hash-paired, 601 singletons, 12822 discordant, 365278 orphans, 10679 too large [>5000 bp], 21992586 duplicates)
Reads: 132188485 total, 64254 skipped (flags/unmapped)
Fragments: 66252554 total (65794660 tlen-paired, 5718 hash-paired, 438 singletons, 19105 discordant, 432633 orphans, 26097 too large [>5000 bp], 24721454 duplicates)
Reads: 133967782 total, 112293 skipped (flags/unmapped)
Fragments: 67271408 total (66212515 tlen-paired, 5207 hash-paired, 517 singletons, 203197 discordant, 849972 orphans, 81581 too large [>5000 bp], 25120813 duplicates)