Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BEOC-N1-BDNA-1_A23TY7KLT4_1/1241_BEOC-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/f433251933b6ea18b49fa4687ef932/.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/d9/f433251933b6ea18b49fa4687ef932/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BEOC-N1-BDNA-1_A23TY7KLT4_1/1241_BEOC-N1-BDNA-1_A23TY7KLT4_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_BEOC-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BEOC-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BEOC-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BEOC-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: 83931210 total, 62896 skipped (flags/unmapped)
Fragments: 42060412 total (41768468 tlen-paired, 3595 hash-paired, 401 singletons, 13645 discordant, 274303 orphans, 11097 too large [>5000 bp], 15656804 duplicates)
Reads: 89923661 total, 51455 skipped (flags/unmapped)
Fragments: 45070996 total (44771482 tlen-paired, 2534 hash-paired, 390 singletons, 9300 discordant, 287290 orphans, 8947 too large [>5000 bp], 16464208 duplicates)
Reads: 89181891 total, 54133 skipped (flags/unmapped)
Fragments: 44702761 total (44379747 tlen-paired, 3404 hash-paired, 298 singletons, 11212 discordant, 308100 orphans, 15317 too large [>5000 bp], 16728797 duplicates)
Reads: 98514541 total, 87013 skipped (flags/unmapped)
Fragments: 49474866 total (48652941 tlen-paired, 2696 hash-paired, 421 singletons, 161539 discordant, 657269 orphans, 67743 too large [>5000 bp], 18527868 duplicates)