Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/e5497763cf98049e20d82abeb3b8fd/.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/1e/e5497763cf98049e20d82abeb3b8fd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_Q4Z-N1-BDNA-1_A23TY7KLT4_1/1241_Q4Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_Q4Z-N1-BDNA-1_A23TY7KLT4_1/1241_Q4Z-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_Q4Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Q4Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Q4Z-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_Q4Z-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: 60906991 total, 34177 skipped (flags/unmapped)
Fragments: 30526472 total (30314324 tlen-paired, 2443 hash-paired, 219 singletons, 6787 discordant, 202699 orphans, 11394 too large [>5000 bp], 9884583 duplicates)
Reads: 57011759 total, 39406 skipped (flags/unmapped)
Fragments: 28566931 total (28381574 tlen-paired, 2596 hash-paired, 218 singletons, 7400 discordant, 175143 orphans, 6926 too large [>5000 bp], 9246316 duplicates)
Reads: 61001133 total, 33267 skipped (flags/unmapped)
Fragments: 30568963 total (30378665 tlen-paired, 2392 hash-paired, 262 singletons, 5362 discordant, 182282 orphans, 6242 too large [>5000 bp], 9678185 duplicates)
Reads: 66979233 total, 56252 skipped (flags/unmapped)
Fragments: 33633354 total (33094089 tlen-paired, 1761 hash-paired, 235 singletons, 106123 discordant, 431146 orphans, 43827 too large [>5000 bp], 10919206 duplicates)