.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE (HCC1395_tumor_vs_HCC1395_BL)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/6fa8e35b23558eaa625bcee67ce3be/.command.log
Size: 5.1 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE (HCC1395_tumor_vs_HCC1395_BL)
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/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.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/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/6fa8e35b23558eaa625bcee67ce3be/.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/HCC1395_tumor/HCC1395_tumor.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/HCC1395_BL/HCC1395_BL.recalibrated.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/c9/6fa8e35b23558eaa625bcee67ce3be/.command.run
==> STAGING COMPLETE (8 inputs)

Running in single sample mode!
Generating vectors for sample:
1. HCC1395_tumor_vs_HCC1395_BL
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.baiThe 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/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.baiThe index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.baiThe index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai



[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.baiThe index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/HCC1395_BL.recalibrated.bam.bai
Evaluating Samples, Lets go!!!
HCC1395_tumor_vs_HCC1395_BL	[0.08685098588466644, 0.08645568788051605, 0.010554153472185135, 0.0005924882716499269, 0.6671572327613831, 0.002909271977841854, 0.04314965754747391, 0.0005491527263075113, 0.00018119681044481695, 0.0002868740411940962]
/usr/local/lib/python3.11/site-packages/main/evaluate_sample.py:47: UserWarning: Sample name 'HCC1395_tumor_vs_HCC1395_BL' has multiple '_' characters; cannot split into tumor/normal IDs. Reporting full name as tumor ID.
  warnings.warn(
Analysis Complete!