Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_B09H-N1-BDNA-1_A23TY7KLT4_1/1241_B09H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/8fa4e2fa5f8fadb14b326c17148467/.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/fc/8fa4e2fa5f8fadb14b326c17148467/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_B09H-N1-BDNA-1_A23TY7KLT4_1/1241_B09H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_B09H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B09H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_B09H-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B09H-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: 70289749 total, 50676 skipped (flags/unmapped)
Fragments: 35204653 total (35003986 tlen-paired, 2965 hash-paired, 309 singletons, 11055 discordant, 186338 orphans, 8207 too large [>5000 bp], 11285222 duplicates)
Reads: 75112886 total, 44587 skipped (flags/unmapped)
Fragments: 37622644 total (37419047 tlen-paired, 4306 hash-paired, 288 singletons, 9224 discordant, 189779 orphans, 6539 too large [>5000 bp], 12129649 duplicates)
Reads: 75928626 total, 41324 skipped (flags/unmapped)
Fragments: 38033890 total (37829394 tlen-paired, 2128 hash-paired, 323 singletons, 7640 discordant, 194405 orphans, 7125 too large [>5000 bp], 11964088 duplicates)
Reads: 82315987 total, 73213 skipped (flags/unmapped)
Fragments: 41291666 total (40764771 tlen-paired, 2462 hash-paired, 296 singletons, 100655 discordant, 423482 orphans, 41610 too large [>5000 bp], 13322092 duplicates)