Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/fe4986fd6dadc1dddbd1c79b4a0711/.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/a3/fe4986fd6dadc1dddbd1c79b4a0711/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_SPC-N1-BDNA-1_B2377KTLT3_1/869_SPC-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_SPC-N1-BDNA-1_B2377KTLT3_1/869_SPC-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_SPC-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_SPC-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_SPC-N1-BDNA-1_B2377KTLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_SPC-N1-BDNA-1_B2377KTLT3_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: 92127597 total, 77367 skipped (flags/unmapped)
Fragments: 46215677 total (45782605 tlen-paired, 31283 hash-paired, 6397 singletons, 9947 discordant, 385445 orphans, 5359 too large [>5000 bp], 10480258 duplicates)
Reads: 100966373 total, 72708 skipped (flags/unmapped)
Fragments: 50655356 total (50176902 tlen-paired, 32946 hash-paired, 6985 singletons, 7399 discordant, 431124 orphans, 10531 too large [>5000 bp], 11524725 duplicates)
Reads: 104359346 total, 134978 skipped (flags/unmapped)
Fragments: 52554421 total (51156484 tlen-paired, 36543 hash-paired, 7204 singletons, 264322 discordant, 1089868 orphans, 106299 too large [>5000 bp], 11820626 duplicates)
Reads: 101997680 total, 74445 skipped (flags/unmapped)
Fragments: 51166647 total (50676805 tlen-paired, 33857 hash-paired, 6913 singletons, 10298 discordant, 438774 orphans, 17814 too large [>5000 bp], 11553027 duplicates)