Downloading: s3://natera-platform-sandbox/pipeline-resources/mimsi/1500_dropped_panel_with_boosted_msi_regions.tsv
  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/23/e9037f7925e4ac39ffabfbee3a34b0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/67b2f0e91ea561f47eaf645e5fc329/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/67b2f0e91ea561f47eaf645e5fc329/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/mimsi/mi_msi_v0_4_0_200x_attn.model
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/e9037f7925e4ac39ffabfbee3a34b0/.command.run
==> STAGING COMPLETE (8 inputs)

Running in single sample mode!
Generating vectors for sample:
1. negative_somatic_control_1
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.baiThe index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai

The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878-downsampled-500k.bam.bai
Sample %s did not have any microsatellites above the required threshold level. 
 negative_somatic_control_1
Evaluating Samples, Lets go!!!
Analysis Complete!
ls: cannot access 'negative_somatic_control_1_results.npy': No such file or directory