Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_TC0-N1-BDNA-1_A23TY32LT4_1/1241_TC0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/2ce58d808f047c72b115cc0f30e4db/.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/20/2ce58d808f047c72b115cc0f30e4db/.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_TC0-N1-BDNA-1_A23TY32LT4_1/1241_TC0-N1-BDNA-1_A23TY32LT4_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_TC0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_TC0-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_TC0-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_TC0-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: 105965188 total, 78823 skipped (flags/unmapped)
Fragments: 53126280 total (52706475 tlen-paired, 5588 hash-paired, 481 singletons, 19088 discordant, 394648 orphans, 14467 too large [>5000 bp], 21650217 duplicates)
Reads: 113881885 total, 62402 skipped (flags/unmapped)
Fragments: 57102656 total (56676392 tlen-paired, 4259 hash-paired, 540 singletons, 13188 discordant, 408277 orphans, 11494 too large [>5000 bp], 23095127 duplicates)
Reads: 125888689 total, 119103 skipped (flags/unmapped)
Fragments: 63273963 total (62072239 tlen-paired, 5331 hash-paired, 463 singletons, 230901 discordant, 965029 orphans, 93576 too large [>5000 bp], 26000544 duplicates)
Reads: 124774762 total, 69372 skipped (flags/unmapped)
Fragments: 62568686 total (62059283 tlen-paired, 4706 hash-paired, 405 singletons, 19963 discordant, 484329 orphans, 26376 too large [>5000 bp], 25756689 duplicates)