Downloading: s3://natera-platform-sandbox/pipeline-resources/mimsi/1500_dropped_panel_with_boosted_msi_regions.tsv
  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/6d/d6da714049324856415d4fcbfe34dc/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed
  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_tumor/HCC1395_tumor.recal.bam.bai
  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_tumor/HCC1395_tumor.recal.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/d6da714049324856415d4fcbfe34dc/.command.run
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==> STAGING COMPLETE (8 inputs)

msi -b 2 -d 1500_dropped_panel_with_boosted_msi_regions.tsv -e xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed -t HCC1395_tumor.recal.bam -n HCC1395_BL.recal.bam -o HCC1395_tumor_vs_HCC1395_BL_xgen Start at:  Thu Jun  4 19:31:38 2026

loading bed regions ...
loading homopolymer and microsatellite sites ...

Total loading windows:  1 


Total loading homopolymer and microsatellites:  1 

window: 0 done...:chr21:28965883-28967883

*** Summary information ***

Number of total sites: 1
Number of sites with enough coverage: 1
Number of MSI sites: 0
MSI score(%): 0

Total time consumed:  0 secs