Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_RZE-N1-BDNA-1_A23TY32LT4_1/1241_RZE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/592af0e8fcfd3da6ae16ad9476d861/.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/19/592af0e8fcfd3da6ae16ad9476d861/.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_RZE-N1-BDNA-1_A23TY32LT4_1/1241_RZE-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_RZE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_RZE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_RZE-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_RZE-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: 100461306 total, 58393 skipped (flags/unmapped)
Fragments: 50377283 total (49961805 tlen-paired, 5629 hash-paired, 330 singletons, 13064 discordant, 396455 orphans, 22566 too large [>5000 bp], 19989185 duplicates)
Reads: 93471026 total, 67210 skipped (flags/unmapped)
Fragments: 46864319 total (46495754 tlen-paired, 4104 hash-paired, 419 singletons, 15609 discordant, 348433 orphans, 12015 too large [>5000 bp], 18455421 duplicates)
Reads: 101381917 total, 57373 skipped (flags/unmapped)
Fragments: 50834574 total (50452978 tlen-paired, 3573 hash-paired, 475 singletons, 10811 discordant, 366737 orphans, 11304 too large [>5000 bp], 19727300 duplicates)
Reads: 111265622 total, 109571 skipped (flags/unmapped)
Fragments: 55922640 total (54842688 tlen-paired, 4530 hash-paired, 368 singletons, 213659 discordant, 861395 orphans, 86267 too large [>5000 bp], 22151573 duplicates)