Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_3I9-N1-BDNA-1_A23H3NYLT3_1/1136_3I9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/32686b29f22fb0ff7afa9a035d58cd/.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/4d/32686b29f22fb0ff7afa9a035d58cd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260302_LH00166_0256_A23H3NYLT3__444aee1e--20260303-100014/alignments/recalibrated/1136_3I9-N1-BDNA-1_A23H3NYLT3_1/1136_3I9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam
==> 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: 1136_3I9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3I9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3I9-N1-BDNA-1_A23H3NYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3I9-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: 91105765 total, 73942 skipped (flags/unmapped)
Fragments: 45676794 total (45289445 tlen-paired, 28990 hash-paired, 8558 singletons, 7894 discordant, 341907 orphans, 14350 too large [>5000 bp], 6947899 duplicates)
Reads: 98341121 total, 68829 skipped (flags/unmapped)
Fragments: 49318247 total (48888654 tlen-paired, 29888 hash-paired, 9012 singletons, 8557 discordant, 382136 orphans, 13473 too large [>5000 bp], 7438828 duplicates)
Reads: 98916104 total, 68803 skipped (flags/unmapped)
Fragments: 49610175 total (49170504 tlen-paired, 31974 hash-paired, 8645 singletons, 6726 discordant, 392326 orphans, 13961 too large [>5000 bp], 7457409 duplicates)
Reads: 98864062 total, 110527 skipped (flags/unmapped)
Fragments: 49777577 total (48532184 tlen-paired, 30006 hash-paired, 8930 singletons, 232352 discordant, 974105 orphans, 90708 too large [>5000 bp], 7451847 duplicates)