.command.log - Workdir - DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:MIMSI_ANALYZE (positive_somatic_control_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/2c168247c23bd2bc2914fe8d9cb0c6/.command.log
Size: 4.6 KB
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:MIMSI_ANALYZE (positive_somatic_control_1)
Attempt
Content

  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/ee/6cac9572c59c95623b798b3d35c5c3/HCC1395_tumor.recalibrated.bam.bai
  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/a5/2c168247c23bd2bc2914fe8d9cb0c6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/6cac9572c59c95623b798b3d35c5c3/HCC1395_tumor.recalibrated.bam
  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/a5/2c168247c23bd2bc2914fe8d9cb0c6/.command.run
==> STAGING COMPLETE (8 inputs)

Running in single sample mode!
Generating vectors for sample:
1. positive_somatic_control_1
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.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
[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. 
 positive_somatic_control_1
Evaluating Samples, Lets go!!!
Analysis Complete!
ls: cannot access 'positive_somatic_control_1_results.npy': No such file or directory