Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/b7403aadd2eb0c2e5989f832f63171/.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/e1/b7403aadd2eb0c2e5989f832f63171/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_2RG-N1-BDNA-1_A23KFG7LT4_1/1029_2RG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_2RG-N1-BDNA-1_A23KFG7LT4_1/1029_2RG-N1-BDNA-1_A23KFG7LT4_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: 1029_2RG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_2RG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2RG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_2RG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 56068957 total, 42785 skipped (flags/unmapped)
Fragments: 28174171 total (27822081 tlen-paired, 2409 hash-paired, 310 singletons, 10735 discordant, 338636 orphans, 8388 too large [>5000 bp], 9362079 duplicates)
Reads: 59659956 total, 36363 skipped (flags/unmapped)
Fragments: 29984889 total (29599538 tlen-paired, 2776 hash-paired, 267 singletons, 9140 discordant, 373168 orphans, 13625 too large [>5000 bp], 9958532 duplicates)
Reads: 60232208 total, 34234 skipped (flags/unmapped)
Fragments: 30269077 total (29905876 tlen-paired, 1864 hash-paired, 329 singletons, 7521 discordant, 353487 orphans, 6818 too large [>5000 bp], 9721365 duplicates)
Reads: 66365012 total, 59787 skipped (flags/unmapped)
Fragments: 33506303 total (32380002 tlen-paired, 2602 hash-paired, 334 singletons, 226628 discordant, 896737 orphans, 94845 too large [>5000 bp], 11077001 duplicates)