Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/c4e3920b151ccb9697118be46f46e7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_XNF-N1-BDNA-1_B2377KTLT3_2/869_XNF-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  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/5d/c4e3920b151ccb9697118be46f46e7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_XNF-N1-BDNA-1_B2377KTLT3_2/869_XNF-N1-BDNA-1_B2377KTLT3_2.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: 869_XNF-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 869_XNF-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XNF-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XNF-N1-BDNA-1_B2377KTLT3_2.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: 79006863 total, 74380 skipped (flags/unmapped)
Fragments: 39706439 total (39183328 tlen-paired, 11927 hash-paired, 6218 singletons, 6873 discordant, 498093 orphans, 11958 too large [>5000 bp], 9374825 duplicates)
Reads: 86220506 total, 65377 skipped (flags/unmapped)
Fragments: 43359223 total (42759731 tlen-paired, 11799 hash-paired, 6582 singletons, 5154 discordant, 575957 orphans, 9611 too large [>5000 bp], 10229870 duplicates)
Reads: 87016797 total, 66252 skipped (flags/unmapped)
Fragments: 43755317 total (43150388 tlen-paired, 13529 hash-paired, 6664 singletons, 6873 discordant, 577863 orphans, 12219 too large [>5000 bp], 10263726 duplicates)
Reads: 89698395 total, 114849 skipped (flags/unmapped)
Fragments: 45416134 total (43486251 tlen-paired, 13274 hash-paired, 7016 singletons, 377165 discordant, 1532428 orphans, 145361 too large [>5000 bp], 10501792 duplicates)