.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE (1173_DXK-T1-TDNA-01_B23T7FYLT4_1_vs_1173_DXK-N1-BDNA-01_B23T7FYLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/b4e4eadd0b8c0ae3190723003c3325/.command.log
Size: 5.9 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE (1173_DXK-T1-TDNA-01_B23T7FYLT4_1_vs_1173_DXK-N1-BDNA-01_B23T7FYLT4_1)
Attempt
Content

  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1173_DXK-T1-TDNA-01_B23T7FYLT4_1/1173_DXK-T1-TDNA-01_B23T7FYLT4_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/8a/b4e4eadd0b8c0ae3190723003c3325/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1173_DXK-N1-BDNA-01_B23T7FYLT4_1/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1173_DXK-N1-BDNA-01_B23T7FYLT4_1/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.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/8a/b4e4eadd0b8c0ae3190723003c3325/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260417_LH00166_0292_B23T7FYLT4__0ce77ad5--20260420-091011/alignments/recalibrated/1173_DXK-T1-TDNA-01_B23T7FYLT4_1/1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam
==> STAGING COMPLETE (8 inputs)

Running in single sample mode!
Generating vectors for sample:
1. 1173_DXK-T1-TDNA-01_B23T7FYLT4_1_vs_1173_DXK-N1-BDNA-01_B23T7FYLT4_1
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_DXK-T1-TDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: normal/1173_DXK-N1-BDNA-01_B23T7FYLT4_1.recalibrated.bam.bai
Evaluating Samples, Lets go!!!
1173_DXK-T1-TDNA-01_B23T7FYLT4_1_vs_1173_DXK-N1-BDNA-01_B23T7FYLT4_1	[0.09635193645954132, 0.08289587497711182, 0.09849119186401367, 0.07909435778856277, 0.07475592195987701, 0.07979249954223633, 0.1394270658493042, 0.08351150900125504, 0.06107969954609871, 0.12056773155927658]
/usr/local/lib/python3.11/site-packages/main/evaluate_sample.py:47: UserWarning: Sample name '1173_DXK-T1-TDNA-01_B23T7FYLT4_1_vs_1173_DXK-N1-BDNA-01_B23T7FYLT4_1' has multiple '_' characters; cannot split into tumor/normal IDs. Reporting full name as tumor ID.
  warnings.warn(
Analysis Complete!