.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/81/9d24eecb3aa5fc7ea8a8c3ca16f5f9/.command.log
Size: 5.2 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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
  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/81/9d24eecb3aa5fc7ea8a8c3ca16f5f9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.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/81/9d24eecb3aa5fc7ea8a8c3ca16f5f9/.command.run
==> 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.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/Sig_18_Blood.recalibrated.bam.bai
Evaluating Samples, Lets go!!!
custom_Sig_18_tumor_normal	[0.0017214687541127205, 0.699863076210022, 0.001862337114289403, 0.0025863538030534983, 0.0008737842435948551, 0.970743715763092, 0.0027642562054097652, 0.0011484759161248803, 0.006529498379677534, 0.0005059506511315703]
/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!