Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/b6158c8992c30a760bcb3530b01342/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/b6158c8992c30a760bcb3530b01342/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/bed/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed
==> 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: HCC1395_BL.recal.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
The index file is older than the data file: HCC1395_BL.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped)
Fragments: 0 total (0 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 0 duplicates)
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped)
Fragments: 0 total (0 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 0 duplicates)
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped)
Fragments: 0 total (0 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 0 duplicates)
Reads: 1322929 total, 178 skipped (flags/unmapped)
Fragments: 664661 total (664477 tlen-paired, 22 hash-paired, 10 singletons, 0 discordant, 152 orphans, 93 too large [>5000 bp], 145939 duplicates)