Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_I2R-N1-BDNA-1_2375WFLT3_s84/1029_I2R-N1-BDNA-1_2375WFLT3_s84.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_I2R-N1-BDNA-1_2375WFLT3_s84/1029_I2R-N1-BDNA-1_2375WFLT3_s84.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/10e21888a2041b41bb722cb07dbbf0/.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/10e21888a2041b41bb722cb07dbbf0/.command.run
==> 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_I2R-N1-BDNA-1_2375WFLT3_s84.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I2R-N1-BDNA-1_2375WFLT3_s84.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I2R-N1-BDNA-1_2375WFLT3_s84.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I2R-N1-BDNA-1_2375WFLT3_s84.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: 71015960 total, 58030 skipped (flags/unmapped)
Fragments: 35697962 total (35220220 tlen-paired, 3294 hash-paired, 1031 singletons, 10990 discordant, 462427 orphans, 12732 too large [>5000 bp], 10202121 duplicates)
Reads: 70612025 total, 59736 skipped (flags/unmapped)
Fragments: 35494086 total (35029737 tlen-paired, 3609 hash-paired, 1161 singletons, 12749 discordant, 446830 orphans, 6054 too large [>5000 bp], 10240430 duplicates)
Reads: 77657694 total, 55319 skipped (flags/unmapped)
Fragments: 39039879 total (38532271 tlen-paired, 3805 hash-paired, 1154 singletons, 9554 discordant, 493095 orphans, 8433 too large [>5000 bp], 11047197 duplicates)
Reads: 80284372 total, 101849 skipped (flags/unmapped)
Fragments: 40577553 total (39059216 tlen-paired, 3523 hash-paired, 1265 singletons, 300921 discordant, 1212628 orphans, 120655 too large [>5000 bp], 11505288 duplicates)