Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_GZP-N1-BDNA-1_2375WFLT3_s73/1029_GZP-N1-BDNA-1_2375WFLT3_s73.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_GZP-N1-BDNA-1_2375WFLT3_s73/1029_GZP-N1-BDNA-1_2375WFLT3_s73.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/4e3bf3873c091d7c6644f02b7ed1f0/.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/4f/4e3bf3873c091d7c6644f02b7ed1f0/.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_GZP-N1-BDNA-1_2375WFLT3_s73.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GZP-N1-BDNA-1_2375WFLT3_s73.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_GZP-N1-BDNA-1_2375WFLT3_s73.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_GZP-N1-BDNA-1_2375WFLT3_s73.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: 44603394 total, 36986 skipped (flags/unmapped)
Fragments: 22411494 total (22124306 tlen-paired, 2156 hash-paired, 664 singletons, 7104 discordant, 277264 orphans, 10674 too large [>5000 bp], 5549911 duplicates)
Reads: 44332489 total, 38691 skipped (flags/unmapped)
Fragments: 22276834 total (21999296 tlen-paired, 2027 hash-paired, 725 singletons, 8363 discordant, 266423 orphans, 3639 too large [>5000 bp], 5574383 duplicates)
Reads: 48754457 total, 35387 skipped (flags/unmapped)
Fragments: 24498453 total (24199704 tlen-paired, 2614 hash-paired, 741 singletons, 5691 discordant, 289703 orphans, 6304 too large [>5000 bp], 6012919 duplicates)
Reads: 49810570 total, 64640 skipped (flags/unmapped)
Fragments: 25158257 total (24271905 tlen-paired, 2064 hash-paired, 805 singletons, 173724 discordant, 709759 orphans, 69990 too large [>5000 bp], 6194656 duplicates)