Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/9907747f943dfff8870c12f497ae42/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_VB-N1-BDNA-1_A23KFG7LT4_1/1029_VB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  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/18/9907747f943dfff8870c12f497ae42/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_VB-N1-BDNA-1_A23KFG7LT4_1/1029_VB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_VB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_VB-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_VB-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: 71201214 total, 44347 skipped (flags/unmapped)
Fragments: 35683789 total (35446189 tlen-paired, 2551 hash-paired, 309 singletons, 9858 discordant, 224882 orphans, 7240 too large [>5000 bp], 12607960 duplicates)
Reads: 76876866 total, 41419 skipped (flags/unmapped)
Fragments: 38528022 total (38278535 tlen-paired, 3091 hash-paired, 459 singletons, 7175 discordant, 238762 orphans, 9312 too large [>5000 bp], 13213253 duplicates)
Reads: 76118166 total, 44769 skipped (flags/unmapped)
Fragments: 38147724 total (37876362 tlen-paired, 3997 hash-paired, 288 singletons, 9038 discordant, 258039 orphans, 18138 too large [>5000 bp], 13447071 duplicates)
Reads: 83704020 total, 72151 skipped (flags/unmapped)
Fragments: 42036391 total (41342113 tlen-paired, 2289 hash-paired, 388 singletons, 135700 discordant, 555901 orphans, 57688 too large [>5000 bp], 14845482 duplicates)