Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BXDO-N1-BDNA-1_A23TY7KLT4_1/1241_BXDO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/2cb7422603fb8f5590cfee0bee39bb/.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/df/2cb7422603fb8f5590cfee0bee39bb/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BXDO-N1-BDNA-1_A23TY7KLT4_1/1241_BXDO-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] [W::hts_idx_load3] The index file is older than the data file: 1241_BXDO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BXDO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_BXDO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_BXDO-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: 77394387 total, 43843 skipped (flags/unmapped)
Fragments: 38765328 total (38559184 tlen-paired, 3959 hash-paired, 347 singletons, 6333 discordant, 195505 orphans, 7870 too large [>5000 bp], 12873058 duplicates)
Reads: 72270443 total, 52959 skipped (flags/unmapped)
Fragments: 36194049 total (35994407 tlen-paired, 3509 hash-paired, 267 singletons, 8807 discordant, 187059 orphans, 8356 too large [>5000 bp], 12201950 duplicates)
Reads: 84770155 total, 46560 skipped (flags/unmapped)
Fragments: 42463422 total (42215011 tlen-paired, 4757 hash-paired, 286 singletons, 9273 discordant, 234095 orphans, 15566 too large [>5000 bp], 14383700 duplicates)
Reads: 84553102 total, 77289 skipped (flags/unmapped)
Fragments: 42423491 total (41850473 tlen-paired, 2696 hash-paired, 309 singletons, 108829 discordant, 461184 orphans, 45162 too large [>5000 bp], 14394898 duplicates)