Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_VV1-N1-BDNA-1_A23H3NYLT3_1/869_VV1-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/357814c5e318f4cee78227efa3473b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/869_VV1-N1-BDNA-1_A23H3NYLT3_1/869_VV1-N1-BDNA-1_A23H3NYLT3_1.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/7c/357814c5e318f4cee78227efa3473b/.command.run
==> 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_VV1-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VV1-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_VV1-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 869_VV1-N1-BDNA-1_A23H3NYLT3_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: 71664344 total, 61610 skipped (flags/unmapped)
Fragments: 35975971 total (35583679 tlen-paired, 14227 hash-paired, 6868 singletons, 7135 discordant, 364062 orphans, 10861 too large [>5000 bp], 4354117 duplicates)
Reads: 77268018 total, 53095 skipped (flags/unmapped)
Fragments: 38811271 total (38365525 tlen-paired, 14598 hash-paired, 7145 singletons, 5657 discordant, 418346 orphans, 8936 too large [>5000 bp], 4659190 duplicates)
Reads: 78883490 total, 91422 skipped (flags/unmapped)
Fragments: 39832680 total (38483051 tlen-paired, 13987 hash-paired, 7449 singletons, 261712 discordant, 1066481 orphans, 100319 too large [>5000 bp], 4726732 duplicates)
Reads: 77338168 total, 54747 skipped (flags/unmapped)
Fragments: 38839858 total (38399679 tlen-paired, 14988 hash-paired, 7206 singletons, 7166 discordant, 410819 orphans, 10865 too large [>5000 bp], 4669917 duplicates)