Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_FWL-N1-BDNA-1_235YY7LT3_1/1029_FWL-N1-BDNA-1_235YY7LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/87f500172c6c02723937a65293b428/.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/cd/87f500172c6c02723937a65293b428/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260203_LH00527_0049_A235YY7LT3__5d8e7d70--20260228-200337/alignments/recalibrated/1029_FWL-N1-BDNA-1_235YY7LT3_1/1029_FWL-N1-BDNA-1_235YY7LT3_1.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] The index file is older than the data file: 1029_FWL-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.baiThe index file is older than the data file: 1029_FWL-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_FWL-N1-BDNA-1_235YY7LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_FWL-N1-BDNA-1_235YY7LT3_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: 53815448 total, 45102 skipped (flags/unmapped)
Fragments: 27006513 total (26746022 tlen-paired, 3288 hash-paired, 2936 singletons, 6987 discordant, 247280 orphans, 3768 too large [>5000 bp], 6010215 duplicates)
Reads: 58211089 total, 39564 skipped (flags/unmapped)
Fragments: 29213782 total (28938176 tlen-paired, 2281 hash-paired, 3024 singletons, 4826 discordant, 265475 orphans, 6230 too large [>5000 bp], 6379010 duplicates)
Reads: 59068894 total, 42737 skipped (flags/unmapped)
Fragments: 29643159 total (29349866 tlen-paired, 2555 hash-paired, 3048 singletons, 6831 discordant, 280859 orphans, 11873 too large [>5000 bp], 6532453 duplicates)
Reads: 59743965 total, 62234 skipped (flags/unmapped)
Fragments: 30115179 total (29272013 tlen-paired, 2565 hash-paired, 3183 singletons, 159890 discordant, 677528 orphans, 66042 too large [>5000 bp], 6616480 duplicates)