Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/4b04bd10b7d5b3a56b3770d5f33dd3/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_CXK-N1-BDNA-1_B2377KTLT3_3/869_CXK-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/4b04bd10b7d5b3a56b3770d5f33dd3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_CXK-N1-BDNA-1_B2377KTLT3_3/869_CXK-N1-BDNA-1_B2377KTLT3_3.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_CXK-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_CXK-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: 70534186 total, 51874 skipped (flags/unmapped)
Fragments: 35393316 total (35046529 tlen-paired, 21685 hash-paired, 5093 singletons, 4592 discordant, 315417 orphans, 8095 too large [>5000 bp], 6928964 duplicates)
Reads: 64245154 total, 51156 skipped (flags/unmapped)
Fragments: 32239754 total (31905775 tlen-paired, 21585 hash-paired, 4615 singletons, 5614 discordant, 302165 orphans, 10635 too large [>5000 bp], 6282884 duplicates)
Reads: 71995334 total, 89133 skipped (flags/unmapped)
Fragments: 36271795 total (35259396 tlen-paired, 23160 hash-paired, 5277 singletons, 195164 discordant, 788798 orphans, 78343 too large [>5000 bp], 7000402 duplicates)
Reads: 63786773 total, 57612 skipped (flags/unmapped)
Fragments: 31997485 total (31687862 tlen-paired, 20804 hash-paired, 4682 singletons, 6104 discordant, 278033 orphans, 8453 too large [>5000 bp], 6254891 duplicates)