Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_I2U-N1-BDNA-1_2375WFLT3_s85/1029_I2U-N1-BDNA-1_2375WFLT3_s85.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_I2U-N1-BDNA-1_2375WFLT3_s85/1029_I2U-N1-BDNA-1_2375WFLT3_s85.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/2b186fde03c74f814070e0c85999e4/.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/24/2b186fde03c74f814070e0c85999e4/.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_I2U-N1-BDNA-1_2375WFLT3_s85.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_I2U-N1-BDNA-1_2375WFLT3_s85.recalibrated.bam.baiThe index file is older than the data file: 1029_I2U-N1-BDNA-1_2375WFLT3_s85.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_I2U-N1-BDNA-1_2375WFLT3_s85.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: 58077926 total, 53175 skipped (flags/unmapped)
Fragments: 29198286 total (28799936 tlen-paired, 3139 hash-paired, 925 singletons, 12470 discordant, 381816 orphans, 5460 too large [>5000 bp], 8095378 duplicates)
Reads: 58549166 total, 51210 skipped (flags/unmapped)
Fragments: 29435005 total (29023188 tlen-paired, 7042 hash-paired, 1006 singletons, 10201 discordant, 393568 orphans, 11260 too large [>5000 bp], 8075393 duplicates)
Reads: 63646310 total, 49671 skipped (flags/unmapped)
Fragments: 31998076 total (31569874 tlen-paired, 2708 hash-paired, 1007 singletons, 8785 discordant, 415702 orphans, 8598 too large [>5000 bp], 8717508 duplicates)
Reads: 65705792 total, 90981 skipped (flags/unmapped)
Fragments: 33215456 total (31945844 tlen-paired, 3604 hash-paired, 1006 singletons, 250563 discordant, 1014439 orphans, 99672 too large [>5000 bp], 9038441 duplicates)