Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/3bdf0795d418df3349421ee7b643ea/.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/84/3bdf0795d418df3349421ee7b643ea/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BLH5-N1-BDNA-1_2375WFLT3_s37/1029_BLH5-N1-BDNA-1_2375WFLT3_s37.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BLH5-N1-BDNA-1_2375WFLT3_s37/1029_BLH5-N1-BDNA-1_2375WFLT3_s37.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

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_BLH5-N1-BDNA-1_2375WFLT3_s37.recalibrated.bam.bai
The index file is older than the data file: 1029_BLH5-N1-BDNA-1_2375WFLT3_s37.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_BLH5-N1-BDNA-1_2375WFLT3_s37.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BLH5-N1-BDNA-1_2375WFLT3_s37.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: 62927080 total, 54228 skipped (flags/unmapped)
Fragments: 31631420 total (31219533 tlen-paired, 3473 hash-paired, 1121 singletons, 9978 discordant, 397315 orphans, 4224 too large [>5000 bp], 8335104 duplicates)
Reads: 68065597 total, 47203 skipped (flags/unmapped)
Fragments: 34218133 total (33774983 tlen-paired, 2916 hash-paired, 1160 singletons, 7094 discordant, 431980 orphans, 7634 too large [>5000 bp], 8894241 duplicates)
Reads: 70729451 total, 90216 skipped (flags/unmapped)
Fragments: 35767558 total (34381378 tlen-paired, 2468 hash-paired, 1110 singletons, 266411 discordant, 1116191 orphans, 110710 too large [>5000 bp], 9292890 duplicates)
Reads: 69172027 total, 51437 skipped (flags/unmapped)
Fragments: 34770147 total (34310556 tlen-paired, 4230 hash-paired, 1105 singletons, 9809 discordant, 444447 orphans, 12924 too large [>5000 bp], 9081074 duplicates)