Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/51b868760933d9bf61838311819080/.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/63/51b868760933d9bf61838311819080/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_I3K-N1-BDNA-1_B23L5TMLT4_1/1029_I3K-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_I3K-N1-BDNA-1_B23L5TMLT4_1/1029_I3K-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
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_I3K-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_I3K-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_I3K-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I3K-N1-BDNA-1_B23L5TMLT4_1.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: 84824152 total, 71948 skipped (flags/unmapped)
Fragments: 42603410 total (42100214 tlen-paired, 4423 hash-paired, 473 singletons, 14989 discordant, 483311 orphans, 14584 too large [>5000 bp], 17136811 duplicates)
Reads: 90507744 total, 59898 skipped (flags/unmapped)
Fragments: 45466335 total (44943506 tlen-paired, 3964 hash-paired, 603 singletons, 10577 discordant, 507685 orphans, 11732 too large [>5000 bp], 17977568 duplicates)
Reads: 99199388 total, 70166 skipped (flags/unmapped)
Fragments: 49831998 total (49220104 tlen-paired, 4355 hash-paired, 461 singletons, 16227 discordant, 590851 orphans, 28269 too large [>5000 bp], 20093917 duplicates)
Reads: 100808792 total, 122317 skipped (flags/unmapped)
Fragments: 50869959 total (49222344 tlen-paired, 4311 hash-paired, 545 singletons, 323551 discordant, 1319208 orphans, 133155 too large [>5000 bp], 20334789 duplicates)