Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BB2O-N1-BDNA-1_A23KFG7LT4_1/1029_BB2O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/0c4c5fba5887436197bf5d70a27bc3/.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/9c/0c4c5fba5887436197bf5d70a27bc3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_BB2O-N1-BDNA-1_A23KFG7LT4_1/1029_BB2O-N1-BDNA-1_A23KFG7LT4_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: 1029_BB2O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BB2O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BB2O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BB2O-N1-BDNA-1_A23KFG7LT4_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: 69056727 total, 40749 skipped (flags/unmapped)
Fragments: 34685766 total (34300279 tlen-paired, 2393 hash-paired, 397 singletons, 8624 discordant, 374073 orphans, 9458 too large [>5000 bp], 11580563 duplicates)
Reads: 64869143 total, 45504 skipped (flags/unmapped)
Fragments: 32583722 total (32202994 tlen-paired, 3251 hash-paired, 418 singletons, 12718 discordant, 364341 orphans, 10477 too large [>5000 bp], 11151266 duplicates)
Reads: 77306743 total, 69613 skipped (flags/unmapped)
Fragments: 39003476 total (37794442 tlen-paired, 2952 hash-paired, 363 singletons, 237272 discordant, 968447 orphans, 99494 too large [>5000 bp], 13333619 duplicates)
Reads: 75853989 total, 45367 skipped (flags/unmapped)
Fragments: 38103827 total (37650230 tlen-paired, 5605 hash-paired, 311 singletons, 12794 discordant, 434887 orphans, 18083 too large [>5000 bp], 13071854 duplicates)