Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/6c14ed1af6fd9750c6a62b444373d9/.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/c2/6c14ed1af6fd9750c6a62b444373d9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_HIF-N1-BDNA-1_A23TY7KLT4_1/1241_HIF-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_HIF-N1-BDNA-1_A23TY7KLT4_1/1241_HIF-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] The index file is older than the data file: 1241_HIF-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_HIF-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_HIF-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_HIF-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: 72805697 total, 51479 skipped (flags/unmapped)
Fragments: 36473315 total (36250165 tlen-paired, 3034 hash-paired, 303 singletons, 10138 discordant, 209675 orphans, 8783 too large [>5000 bp], 12120570 duplicates)
Reads: 78494146 total, 44052 skipped (flags/unmapped)
Fragments: 39325399 total (39097238 tlen-paired, 2729 hash-paired, 312 singletons, 7156 discordant, 217964 orphans, 8786 too large [>5000 bp], 12826082 duplicates)
Reads: 77764991 total, 45151 skipped (flags/unmapped)
Fragments: 38960521 total (38720983 tlen-paired, 3405 hash-paired, 257 singletons, 8479 discordant, 227397 orphans, 13226 too large [>5000 bp], 13012969 duplicates)
Reads: 85412128 total, 73308 skipped (flags/unmapped)
Fragments: 42869212 total (42244971 tlen-paired, 2040 hash-paired, 374 singletons, 122111 discordant, 499716 orphans, 50243 too large [>5000 bp], 14309518 duplicates)