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/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/959e2bb156b259d2a42b0653c3665b/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam
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/HCC1395_BL/HCC1395_BL.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/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/959e2bb156b259d2a42b0653c3665b/.command.run
==> 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.recalibrated.bam -n HCC1395_BL.recalibrated.bam -o HCC1395_tumor_vs_HCC1395_BL_xgen Start at: Mon Jun 8 20:42:48 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