.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/5d/80e521fcc2ae77d6621da24d3eab3e/.command.log
Size: 5.0 KB
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:MIMSI_ANALYZE (positive_somatic_control_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/2d1ee30ded13138a2cedbdce9a2948/NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/2d1ee30ded13138a2cedbdce9a2948/NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
  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/5d/80e521fcc2ae77d6621da24d3eab3e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878.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/5d/80e521fcc2ae77d6621da24d3eab3e/.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: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai

[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/reference-NA12878.bam.bai
Evaluating Samples, Lets go!!!
positive_somatic_control_1	[0.018430830910801888, 0.027202313765883446, 0.035082120448350906, 0.03339703008532524, 0.019277920946478844, 0.0436033234000206, 0.046199601143598557, 0.03397910296916962, 0.03747733682394028, 0.035198356956243515]
/usr/local/lib/python3.11/site-packages/main/evaluate_sample.py:47: UserWarning: Sample name 'positive_somatic_control_1' has multiple '_' characters; cannot split into tumor/normal IDs. Reporting full name as tumor ID.
  warnings.warn(
Analysis Complete!