Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_PXA-N1-BDNA-1_A23TY7KLT4_1/1241_PXA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/95907a29ba1f844431b7f7f3fa9927/.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/c1/95907a29ba1f844431b7f7f3fa9927/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_PXA-N1-BDNA-1_A23TY7KLT4_1/1241_PXA-N1-BDNA-1_A23TY7KLT4_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_PXA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_PXA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_PXA-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_PXA-N1-BDNA-1_A23TY7KLT4_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: 95048973 total, 53532 skipped (flags/unmapped)
Fragments: 47622433 total (47317743 tlen-paired, 8137 hash-paired, 290 singletons, 11536 discordant, 284727 orphans, 17796 too large [>5000 bp], 17201265 duplicates)
Reads: 89237973 total, 63624 skipped (flags/unmapped)
Fragments: 44697932 total (44433273 tlen-paired, 5507 hash-paired, 354 singletons, 12767 discordant, 246031 orphans, 12435 too large [>5000 bp], 16094714 duplicates)
Reads: 96027479 total, 52249 skipped (flags/unmapped)
Fragments: 48104544 total (47837039 tlen-paired, 3935 hash-paired, 417 singletons, 9118 discordant, 254035 orphans, 10297 too large [>5000 bp], 16992276 duplicates)
Reads: 104569737 total, 87469 skipped (flags/unmapped)
Fragments: 52468958 total (51756079 tlen-paired, 3348 hash-paired, 368 singletons, 137965 discordant, 571198 orphans, 57959 too large [>5000 bp], 18985166 duplicates)