Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/2968bde31a0b9f873062eb5cc9cc1f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_T05-N1-BDNA-1_B23KGCJLT4_1/1029_T05-N1-BDNA-1_B23KGCJLT4_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/2c/2968bde31a0b9f873062eb5cc9cc1f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_T05-N1-BDNA-1_B23KGCJLT4_1/1029_T05-N1-BDNA-1_B23KGCJLT4_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_T05-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_T05-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_T05-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_T05-N1-BDNA-1_B23KGCJLT4_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: 71387197 total, 52835 skipped (flags/unmapped)
Fragments: 35771462 total (35525797 tlen-paired, 3201 hash-paired, 271 singletons, 13494 discordant, 228699 orphans, 10204 too large [>5000 bp], 12990040 duplicates)
Reads: 84256798 total, 48076 skipped (flags/unmapped)
Fragments: 42226293 total (41925366 tlen-paired, 4725 hash-paired, 275 singletons, 15100 discordant, 280827 orphans, 18619 too large [>5000 bp], 15418682 duplicates)
Reads: 76161349 total, 41340 skipped (flags/unmapped)
Fragments: 38166865 total (37923934 tlen-paired, 2334 hash-paired, 424 singletons, 9220 discordant, 230953 orphans, 8828 too large [>5000 bp], 13626769 duplicates)
Reads: 84516789 total, 72134 skipped (flags/unmapped)
Fragments: 42426930 total (41795737 tlen-paired, 1759 hash-paired, 314 singletons, 118735 discordant, 510385 orphans, 50747 too large [>5000 bp], 15519120 duplicates)