Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/668fcf4b4b4509b92e9bc281a5927e/.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/cf/668fcf4b4b4509b92e9bc281a5927e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_1UH-N1-BDNA-1_A23TY7KLT4_1/1241_1UH-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_1UH-N1-BDNA-1_A23TY7KLT4_1/1241_1UH-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_1UH-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_1UH-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_1UH-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] 
The index file is older than the data file: 1241_1UH-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: 89800789 total, 47398 skipped (flags/unmapped)
Fragments: 45005722 total (44716123 tlen-paired, 2989 hash-paired, 447 singletons, 9871 discordant, 276292 orphans, 9343 too large [>5000 bp], 14314352 duplicates)
Reads: 83262208 total, 58804 skipped (flags/unmapped)
Fragments: 41728369 total (41439167 tlen-paired, 3599 hash-paired, 402 singletons, 14615 discordant, 270586 orphans, 8827 too large [>5000 bp], 13409811 duplicates)
Reads: 98086845 total, 82819 skipped (flags/unmapped)
Fragments: 49258413 total (48470576 tlen-paired, 2167 hash-paired, 351 singletons, 149414 discordant, 635905 orphans, 61728 too large [>5000 bp], 16018026 duplicates)
Reads: 97352069 total, 53605 skipped (flags/unmapped)
Fragments: 48792323 total (48463639 tlen-paired, 6829 hash-paired, 324 singletons, 14183 discordant, 307348 orphans, 10745 too large [>5000 bp], 15880165 duplicates)