Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/e86037603ba3b9e6f0d5998f4853dd/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_HQU-N1-BDNA-1_A23TY32LT4_1/1029_HQU-N1-BDNA-1_A23TY32LT4_1.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/9e/e86037603ba3b9e6f0d5998f4853dd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1029_HQU-N1-BDNA-1_A23TY32LT4_1/1029_HQU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
==> 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_HQU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HQU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HQU-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_HQU-N1-BDNA-1_A23TY32LT4_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: 62451801 total, 48709 skipped (flags/unmapped)
Fragments: 31342959 total (31032884 tlen-paired, 2393 hash-paired, 224 singletons, 7664 discordant, 299794 orphans, 8596 too large [>5000 bp], 12058354 duplicates)
Reads: 67288375 total, 41990 skipped (flags/unmapped)
Fragments: 33784971 total (33423470 tlen-paired, 4643 hash-paired, 232 singletons, 7095 discordant, 349531 orphans, 13103 too large [>5000 bp], 13041830 duplicates)
Reads: 68065300 total, 41232 skipped (flags/unmapped)
Fragments: 34170323 total (33831198 tlen-paired, 1901 hash-paired, 334 singletons, 5388 discordant, 331502 orphans, 7629 too large [>5000 bp], 12881777 duplicates)
Reads: 75057534 total, 83835 skipped (flags/unmapped)
Fragments: 37821963 total (36756165 tlen-paired, 2696 hash-paired, 315 singletons, 218543 discordant, 844244 orphans, 87166 too large [>5000 bp], 14482632 duplicates)