Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/e339e1fa107f167c099f8de72de395/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/188b0cba85e80e2ca932fc08e9e8ca/custom_Sig_18_tumor_normal.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/b127b028a63a23e45853da945fb33f/custom_Sig_18_tumor_normal.segments.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/b127b028a63a23e45853da945fb33f/custom_Sig_18_tumor_normal.purity_ploidy.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-66b9fe59-86da-40b2-8dde-3f9f73edb43d/19/aa295d8d07d5c0c679f5f5343a1981/COSMIC_v3.5_SBS_GRCh38.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-66b9fe59-86da-40b2-8dde-3f9f73edb43d/45/ec2a1a6d2472a474b510ba7d57765a/COSMIC_v3.5_ID_GRCh37.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-66b9fe59-86da-40b2-8dde-3f9f73edb43d/0a/5073430441ac7dae45fe60028d7579/COSMIC_v3.5_CN_GRCh37.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/e339e1fa107f167c099f8de72de395/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/188b0cba85e80e2ca932fc08e9e8ca/custom_Sig_18_tumor_normal.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-66b9fe59-86da-40b2-8dde-3f9f73edb43d/6a/ba26afb14dd9cac58ce0ad949e7ca2/tso_fit_cla.v02.rds
==> STAGING COMPLETE (10 inputs)

=== N7 Analysis ===
Sample ID: custom_Sig_18_tumor_normal

Validating inputs...
Classification model provided: tso_fit_cla.v02.rds
All inputs validated successfully.

Loading required packages...
Warning: Your system is mis-configured: '/var/db/timezone/localtime' is not a symlink
Warning: '/var/db/timezone/localtime' is not identical to any known timezone file
Warning message:
Failed to locate timezone database 
Packages loaded.

Output files will be written to:
  cn_features: ./custom_Sig_18_tumor_normal.cn_features.csv
  sbs_features: ./custom_Sig_18_tumor_normal.sbs_features.csv
  indel_features: ./custom_Sig_18_tumor_normal.indel_features.csv
  signature_exposures: ./custom_Sig_18_tumor_normal.signature_exposures.csv
  classification: ./custom_Sig_18_tumor_normal.classification.csv

Starting analysis...
Loading input data...
  Loading CNV segments from FACETS...
    Loaded 3 segments
    WARNING: CN segment count (3) below minimum threshold (10)
  Loading somatic SNVs from VCF...
[W::hts_idx_load3] The index file is older than the data file: custom_Sig_18_tumor_normal.vcf.gz.tbi
Any neighbouring SNVs will be merged into DBS/MBS variants.
Set the 'predefined_dbs_mbs' to 'TRUE' if you don't want this.
    Loaded 9 PASS SNVs
    WARNING: SNV count (9) below minimum threshold (10)
  Loading somatic INDELs from VCF...
[W::hts_idx_load3] The index file is older than the data file: custom_Sig_18_tumor_normal.vcf.gz.tbi
    Loaded 1 PASS INDELs
    WARNING: INDEL count (1) below minimum threshold (10)
  Loading signature definitions...
    CN signatures: 26 signatures, 48 features
    SBS signatures: 97 signatures, 96 features
    INDEL signatures: 25 signatures, 83 features
  Loading classification model...
    Model loaded: list

All input data loaded successfully.

Generating feature matrices...
  Building CN feature matrix...
    CN count below threshold. Generating empty feature matrix.
    CN matrix: 48 features x 1 samples
    Total segments classified: 0

Feature matrices generated successfully.

  Building SBS mutation matrix...
    SBS count below threshold. Generating empty feature matrix.
    SBS matrix: 96 contexts x 1 samples
    Total SNVs in matrix: 0
  Building INDEL context matrix...
    INDEL count below threshold. Generating empty feature matrix.
    INDEL matrix: 83 contexts x 1 samples
    Total INDELs in matrix: 0
Fitting signatures to feature matrices...
  Fitting CN signatures... (total counts: 0)
    WARNING: CN count (0) below minimum threshold (10). Reporting zero exposures.
    Fitted 26 CN signatures
  Fitting SBS signatures... (total counts: 0)
    WARNING: SBS count (0) below minimum threshold (10). Reporting zero exposures.
    Fitted 97 SBS signatures
  Fitting INDEL signatures... (total counts: 0)
    WARNING: INDEL count (0) below minimum threshold (10). Reporting zero exposures.
    Fitted 25 INDEL signatures

Signature fitting complete.
  Total signatures fitted: 148

Calculating cosine similarities with signatures...
  Calculating CN signature similarities...
    WARNING: CN count below threshold. Reporting 0 similarities.
    Compared against 26 CN signatures
  Calculating SBS signature similarities...
    WARNING: SBS count below threshold. Reporting 0 similarities.
    Compared against 97 SBS signatures
  Calculating INDEL signature similarities...
    WARNING: INDEL count below threshold. Reporting 0 similarities.
    Compared against 25 INDEL signatures

Cosine similarity calculations complete.

Combining exposures and similarities...
  Combined 148 signature results

Applying classification model...
  NOTE: All signature exposures are zero - classification based on zero features
  Prediction: 1
  Prediction stability: 100%
  Probability (0): 0.1011
  Probability (1): 0.8989

Writing output files...
  Writing feature matrices...
    Wrote: ./custom_Sig_18_tumor_normal.sbs_features.csv
    Wrote: ./custom_Sig_18_tumor_normal.indel_features.csv
    Wrote: ./custom_Sig_18_tumor_normal.cn_features.csv
  Writing signature exposures...
    Wrote: ./custom_Sig_18_tumor_normal.signature_exposures.csv
  Writing classification results...
    Wrote: ./custom_Sig_18_tumor_normal.classification.csv

=== Analysis Complete ===
Output directory: .