Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_Q3K-N1-BDNA-1_B23H2GYLT3_1/1029_Q3K-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/ea0ccc06e365c655b81c37cf449629/.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/ef/ea0ccc06e365c655b81c37cf449629/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_Q3K-N1-BDNA-1_B23H2GYLT3_1/1029_Q3K-N1-BDNA-1_B23H2GYLT3_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: 1029_Q3K-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Q3K-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Q3K-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_Q3K-N1-BDNA-1_B23H2GYLT3_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: 83491096 total, 74471 skipped (flags/unmapped)
Fragments: 41889329 total (41487507 tlen-paired, 16884 hash-paired, 6804 singletons, 8149 discordant, 369985 orphans, 7378 too large [>5000 bp], 9156409 duplicates)
Reads: 91785371 total, 64364 skipped (flags/unmapped)
Fragments: 46068494 total (45610948 tlen-paired, 17465 hash-paired, 7188 singletons, 5824 discordant, 427069 orphans, 9138 too large [>5000 bp], 10058248 duplicates)
Reads: 91943318 total, 69867 skipped (flags/unmapped)
Fragments: 46141735 total (45679403 tlen-paired, 18297 hash-paired, 7122 singletons, 8540 discordant, 428373 orphans, 12738 too large [>5000 bp], 10050117 duplicates)
Reads: 93798633 total, 121319 skipped (flags/unmapped)
Fragments: 47283373 total (45908039 tlen-paired, 18702 hash-paired, 7603 singletons, 263104 discordant, 1085925 orphans, 102048 too large [>5000 bp], 10219417 duplicates)