Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/f7c3270acb74c67e6ff31cbb591d6f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BJLO-N1-BDNA-1_A23TY7KLT4_1/1241_BJLO-N1-BDNA-1_A23TY7KLT4_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/f7/f7c3270acb74c67e6ff31cbb591d6f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BJLO-N1-BDNA-1_A23TY7KLT4_1/1241_BJLO-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_BJLO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJLO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJLO-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BJLO-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: 75312188 total, 43305 skipped (flags/unmapped)
Fragments: 37738270 total (37486457 tlen-paired, 3755 hash-paired, 220 singletons, 10079 discordant, 237759 orphans, 15161 too large [>5000 bp], 12831176 duplicates)
Reads: 82855765 total, 72256 skipped (flags/unmapped)
Fragments: 41583131 total (40990942 tlen-paired, 2724 hash-paired, 340 singletons, 113256 discordant, 475869 orphans, 46728 too large [>5000 bp], 14198101 duplicates)
Reads: 70591829 total, 48356 skipped (flags/unmapped)
Fragments: 35370662 total (35145668 tlen-paired, 3103 hash-paired, 250 singletons, 11696 discordant, 209945 orphans, 6172 too large [>5000 bp], 11902410 duplicates)
Reads: 76339369 total, 41580 skipped (flags/unmapped)
Fragments: 38248066 total (38020965 tlen-paired, 3812 hash-paired, 302 singletons, 8126 discordant, 214861 orphans, 8410 too large [>5000 bp], 12685534 duplicates)