.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE (custom_Sig_18_tumor_normal)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/bc292858b4313ab8167337e94b447b/.command.log
Size: 4.9 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE (custom_Sig_18_tumor_normal)
Attempt
Content

  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/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/bc292858b4313ab8167337e94b447b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_tissue/Sig_18_tissue.recal.bam.bai
  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/bc292858b4313ab8167337e94b447b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_tissue/Sig_18_tissue.recal.bam
==> STAGING COMPLETE (8 inputs)

Running in single sample mode!
Generating vectors for sample:
1. custom_Sig_18_tumor_normal
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recal.bam.bai
Evaluating Samples, Lets go!!!
custom_Sig_18_tumor_normal	[0.34616386890411377, 0.02704177051782608, 0.9433739185333252, 0.0008938228711485863, 0.013792874291539192, 0.0003802626160904765, 0.98104327917099, 0.08164578676223755, 0.7842073440551758, 0.004908041097223759]
/usr/local/lib/python3.11/site-packages/main/evaluate_sample.py:47: UserWarning: Sample name 'custom_Sig_18_tumor_normal' has multiple '_' characters; cannot split into tumor/normal IDs. Reporting full name as tumor ID.
  warnings.warn(
Analysis Complete!