Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_VJZ-N1-BDNA-1_B2377KTLT3_3/869_VJZ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/510ab02c21dbfbac52c3e6566f44e8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_VJZ-N1-BDNA-1_B2377KTLT3_3/869_VJZ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam
  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/83/510ab02c21dbfbac52c3e6566f44e8/.command.run
==> 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_VJZ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VJZ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VJZ-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VJZ-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: 64739089 total, 68090 skipped (flags/unmapped)
Fragments: 32462532 total (32144216 tlen-paired, 33544 hash-paired, 4658 singletons, 7153 discordant, 272961 orphans, 11777 too large [>5000 bp], 7374856 duplicates)
Reads: 70817746 total, 56855 skipped (flags/unmapped)
Fragments: 35527550 total (35174403 tlen-paired, 35867 hash-paired, 4966 singletons, 5115 discordant, 307199 orphans, 8978 too large [>5000 bp], 8103318 duplicates)
Reads: 71143555 total, 56067 skipped (flags/unmapped)
Fragments: 35695249 total (35320775 tlen-paired, 37027 hash-paired, 5147 singletons, 7217 discordant, 325083 orphans, 13610 too large [>5000 bp], 8097234 duplicates)
Reads: 72830049 total, 104237 skipped (flags/unmapped)
Fragments: 36678659 total (35668906 tlen-paired, 37636 hash-paired, 5270 singletons, 188173 discordant, 778674 orphans, 76219 too large [>5000 bp], 8320087 duplicates)