Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_4J3-N1-BDNA-1_2375WFLT3_s11/1029_4J3-N1-BDNA-1_2375WFLT3_s11.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/a391d9a1641e21cad1b069fcfb67fe/.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/83/a391d9a1641e21cad1b069fcfb67fe/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_4J3-N1-BDNA-1_2375WFLT3_s11/1029_4J3-N1-BDNA-1_2375WFLT3_s11.recalibrated.bam.bai
==> 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_4J3-N1-BDNA-1_2375WFLT3_s11.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_4J3-N1-BDNA-1_2375WFLT3_s11.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4J3-N1-BDNA-1_2375WFLT3_s11.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_4J3-N1-BDNA-1_2375WFLT3_s11.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: 74486213 total, 62984 skipped (flags/unmapped)
Fragments: 37429790 total (36967413 tlen-paired, 3489 hash-paired, 1259 singletons, 12365 discordant, 445264 orphans, 5086 too large [>5000 bp], 11110937 duplicates)
Reads: 80284151 total, 56471 skipped (flags/unmapped)
Fragments: 40348573 total (39850686 tlen-paired, 3319 hash-paired, 1209 singletons, 8462 discordant, 484897 orphans, 8320 too large [>5000 bp], 11781337 duplicates)
Reads: 81740256 total, 62350 skipped (flags/unmapped)
Fragments: 41076024 total (40554439 tlen-paired, 4575 hash-paired, 1187 singletons, 11812 discordant, 504011 orphans, 15528 too large [>5000 bp], 12071183 duplicates)
Reads: 83725246 total, 107587 skipped (flags/unmapped)
Fragments: 42310781 total (40766354 tlen-paired, 2843 hash-paired, 1312 singletons, 298137 discordant, 1242135 orphans, 119772 too large [>5000 bp], 12352640 duplicates)