Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/b5cf793cbe520410c266d22fa43d76/HCC1395_tumor.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/8e83c2bce6a3bead680f1b07721b49/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/b5cf793cbe520410c266d22fa43d76/HCC1395_tumor.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MSISensor2/Homo_sapiens_assembly38_msisesnor2_xgen_intersect_filtered.sites
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/8e83c2bce6a3bead680f1b07721b49/.command.run
==> STAGING COMPLETE (8 inputs)
msi -b 2 -d Homo_sapiens_assembly38_msisesnor2_xgen_intersect_filtered.sites -e xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed -t HCC1395_tumor.recalibrated.bam -n reference-NA12878-downsampled-500k.bam -o positive_somatic_control_1_xgen Start at: Wed May 27 15:31:24 2026
loading bed regions ...
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window: 390 done...:chr9:99150386-99155098
window: 391 done...:chr9:125146807-125150542
window: 392 done...:chr9:127789070-127791792
window: 393 done...:chr9:132893693-132898613
window: 394 done...:chr9:134439091-134441091
window: 395 done...:chrX:1461977-1463977
window: 396 done...:chrX:20124956-20129038
window: 397 done...:chrX:40095514-40097514
window: 398 done...:chrX:41346846-41350900
window: 399 done...:chrX:47165026-47167026
window: 400 done...:chrX:49033954-49035954
window: 401 done...:chrX:53191256-53193256
window: 402 done...:chrX:67695139-67730987
window: 403 done...:chrX:77505897-77635232
window: 404 done...:chrX:103376474-103378474
window: 405 done...:chrX:111219889-111221889
window: 406 done...:chrX:123911216-124101883
window: 407 done...:chrX:129993800-130058652
window: 408 done...:chrX:134395885-134428490
*** Summary information ***
Number of total sites: 1190
Number of sites with enough coverage: 0
Number of MSI sites: 0
MSI score(%): 0
Total time consumed: 4 secs