Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/ffe4f9cbe20d245248043f54b65c77/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BGFD-N1-BDNA-1_2375WFLT3_s30/1029_BGFD-N1-BDNA-1_2375WFLT3_s30.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BGFD-N1-BDNA-1_2375WFLT3_s30/1029_BGFD-N1-BDNA-1_2375WFLT3_s30.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/05/ffe4f9cbe20d245248043f54b65c77/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BGFD-N1-BDNA-1_2375WFLT3_s30.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BGFD-N1-BDNA-1_2375WFLT3_s30.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGFD-N1-BDNA-1_2375WFLT3_s30.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BGFD-N1-BDNA-1_2375WFLT3_s30.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: 49195946 total, 42098 skipped (flags/unmapped)
Fragments: 24730674 total (24404965 tlen-paired, 2181 hash-paired, 865 singletons, 8652 discordant, 314011 orphans, 3688 too large [>5000 bp], 6426267 duplicates)
Reads: 49512997 total, 40636 skipped (flags/unmapped)
Fragments: 24888117 total (24556714 tlen-paired, 2604 hash-paired, 828 singletons, 7636 discordant, 320335 orphans, 8645 too large [>5000 bp], 6403410 duplicates)
Reads: 53381380 total, 38646 skipped (flags/unmapped)
Fragments: 26837349 total (26483569 tlen-paired, 2393 hash-paired, 858 singletons, 6427 discordant, 344102 orphans, 6498 too large [>5000 bp], 6830070 duplicates)
Reads: 55297003 total, 74551 skipped (flags/unmapped)
Fragments: 27951744 total (26886845 tlen-paired, 1956 hash-paired, 972 singletons, 209837 discordant, 852134 orphans, 86035 too large [>5000 bp], 7127696 duplicates)