Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/42b78bf848ad0238a8c75c64b8fdfd/.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/f5/42b78bf848ad0238a8c75c64b8fdfd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BQMQ-N1-BDNA-1_2375WFLT3_s48/1029_BQMQ-N1-BDNA-1_2375WFLT3_s48.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BQMQ-N1-BDNA-1_2375WFLT3_s48/1029_BQMQ-N1-BDNA-1_2375WFLT3_s48.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BQMQ-N1-BDNA-1_2375WFLT3_s48.recalibrated.bam.baiThe index file is older than the data file: 1029_BQMQ-N1-BDNA-1_2375WFLT3_s48.recalibrated.bam.bai

The index file is older than the data file: 1029_BQMQ-N1-BDNA-1_2375WFLT3_s48.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BQMQ-N1-BDNA-1_2375WFLT3_s48.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: 57774443 total, 50284 skipped (flags/unmapped)
Fragments: 29069531 total (28633087 tlen-paired, 2959 hash-paired, 890 singletons, 10066 discordant, 422529 orphans, 4258 too large [>5000 bp], 8031529 duplicates)
Reads: 62768531 total, 46095 skipped (flags/unmapped)
Fragments: 31586090 total (31111874 tlen-paired, 2894 hash-paired, 900 singletons, 7058 discordant, 463364 orphans, 7260 too large [>5000 bp], 8604866 duplicates)
Reads: 64179634 total, 49734 skipped (flags/unmapped)
Fragments: 32291462 total (31796918 tlen-paired, 2559 hash-paired, 923 singletons, 10215 discordant, 480847 orphans, 14373 too large [>5000 bp], 8825604 duplicates)
Reads: 65635233 total, 88876 skipped (flags/unmapped)
Fragments: 33262197 total (31754644 tlen-paired, 2582 hash-paired, 927 singletons, 294138 discordant, 1209906 orphans, 116398 too large [>5000 bp], 8999379 duplicates)