Downloading: s3://natera-platform-sandbox/pipeline-resources/mimsi/1500_dropped_panel_with_boosted_msi_regions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/ebc5ddd6d1c2840a083a49b95b9b7a/.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/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/ebc5ddd6d1c2840a083a49b95b9b7a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
==> 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 Sig_18_tissue.recalibrated.bam -n Sig_18_Blood.recalibrated.bam -o custom_Sig_18_tumor_normal_xgen Start at:  Thu May 28 23:01:10 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