Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/a3275cebf253f43fbb661c865cc9e9/.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/f3/a3275cebf253f43fbb661c865cc9e9/.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_3/869_XNF-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  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_3/869_XNF-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
==> 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_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XNF-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XNF-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_XNF-N1-BDNA-1_B2377KTLT3_3.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: 53303408 total, 55545 skipped (flags/unmapped)
Fragments: 26759546 total (26447200 tlen-paired, 11961 hash-paired, 4243 singletons, 4644 discordant, 291498 orphans, 12256 too large [>5000 bp], 4750733 duplicates)
Reads: 58527534 total, 46817 skipped (flags/unmapped)
Fragments: 29404413 total (29047538 tlen-paired, 11952 hash-paired, 4597 singletons, 3564 discordant, 336762 orphans, 6625 too large [>5000 bp], 5224284 duplicates)
Reads: 58686991 total, 46371 skipped (flags/unmapped)
Fragments: 29485876 total (29120751 tlen-paired, 13234 hash-paired, 4424 singletons, 4807 discordant, 342660 orphans, 7976 too large [>5000 bp], 5195237 duplicates)
Reads: 60184699 total, 78040 skipped (flags/unmapped)
Fragments: 30415001 total (29294701 tlen-paired, 13202 hash-paired, 4826 singletons, 215577 discordant, 886695 orphans, 84089 too large [>5000 bp], 5280742 duplicates)