=== N7 Analysis ===
Sample ID: 1029_0W2

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: ./1029_0W2.cn_features.csv
  sbs_features: ./1029_0W2.sbs_features.csv
  indel_features: ./1029_0W2.indel_features.csv
  signature_exposures: ./1029_0W2.signature_exposures.csv
  classification: ./1029_0W2.classification.csv

Starting analysis...
Loading input data...
  Loading CNV segments from FACETS...
    Loaded 91 segments
  Loading somatic SNVs from VCF...
Any neighbouring SNVs will be merged into DBS/MBS variants.
Set the 'predefined_dbs_mbs' to 'TRUE' if you don't want this.
    Loaded 841 PASS SNVs
  Loading somatic INDELs from VCF...
    Loaded 105 PASS INDELs
  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 matrix: 48 features x 1 samples
    Total segments classified: 78

Feature matrices generated successfully.

  Building SBS mutation matrix...
    SBS matrix: 96 contexts x 1 samples
    Total SNVs in matrix: 818
  Building INDEL context matrix...
    INDEL matrix: 83 contexts x 1 samples
    Total INDELs in matrix: 105
Fitting signatures to feature matrices...
  Fitting CN signatures... (total counts: 78)
Performed 10 of 100 iterations
Performed 20 of 100 iterations
Performed 30 of 100 iterations
Performed 40 of 100 iterations
Performed 50 of 100 iterations
Performed 60 of 100 iterations
Performed 70 of 100 iterations
Performed 80 of 100 iterations
Performed 90 of 100 iterations
Performed 100 of 100 iterations
Warning message:
In `[.data.table`(results, , `:=`(signature_type, signature_type)) :
  A shallow copy of this data.table was taken so that := can add or remove 1 columns by reference. At an earlier point, this data.table was copied by R (or was created manually using structure() or similar). Avoid names<- and attr<- which in R currently (and oddly) may copy the whole data.table. Use set* syntax instead to avoid copying: ?set, ?setnames and ?setattr. It's also not unusual for data.table-agnostic packages to produce tables affected by this issue. If this message doesn't help, please report your use case to the data.table issue tracker so the root cause can be fixed or this message improved.
    Fitted 26 CN signatures
  Fitting SBS signatures... (total counts: 818)
Performed 10 of 100 iterations
Performed 20 of 100 iterations
Performed 30 of 100 iterations
Performed 40 of 100 iterations
Performed 50 of 100 iterations
Performed 60 of 100 iterations
Performed 70 of 100 iterations
Performed 80 of 100 iterations
Performed 90 of 100 iterations
Performed 100 of 100 iterations
Warning message:
In `[.data.table`(results, , `:=`(signature_type, signature_type)) :
  A shallow copy of this data.table was taken so that := can add or remove 1 columns by reference. At an earlier point, this data.table was copied by R (or was created manually using structure() or similar). Avoid names<- and attr<- which in R currently (and oddly) may copy the whole data.table. Use set* syntax instead to avoid copying: ?set, ?setnames and ?setattr. It's also not unusual for data.table-agnostic packages to produce tables affected by this issue. If this message doesn't help, please report your use case to the data.table issue tracker so the root cause can be fixed or this message improved.
    Fitted 97 SBS signatures
  Fitting INDEL signatures... (total counts: 105)
Performed 10 of 100 iterations
Performed 20 of 100 iterations
Performed 30 of 100 iterations
Performed 40 of 100 iterations
Performed 50 of 100 iterations
Performed 60 of 100 iterations
Performed 70 of 100 iterations
Performed 80 of 100 iterations
Performed 90 of 100 iterations
Performed 100 of 100 iterations
Warning message:
In `[.data.table`(results, , `:=`(signature_type, signature_type)) :
  A shallow copy of this data.table was taken so that := can add or remove 1 columns by reference. At an earlier point, this data.table was copied by R (or was created manually using structure() or similar). Avoid names<- and attr<- which in R currently (and oddly) may copy the whole data.table. Use set* syntax instead to avoid copying: ?set, ?setnames and ?setattr. It's also not unusual for data.table-agnostic packages to produce tables affected by this issue. If this message doesn't help, please report your use case to the data.table issue tracker so the root cause can be fixed or this message improved.
    Fitted 25 INDEL signatures

Signature fitting complete.
  Total signatures fitted: 148

Calculating cosine similarities with signatures...
  Calculating CN signature similarities...
    Compared against 26 CN signatures
  Calculating SBS signature similarities...
    Compared against 97 SBS signatures
  Calculating INDEL signature similarities...
    Compared against 25 INDEL signatures

Cosine similarity calculations complete.

Combining exposures and similarities...
  Combined 148 signature results

Applying classification model...
  Prediction: 0
  Prediction stability: 96%
  Probability (0): 1
  Probability (1): 0

Writing output files...
  Writing feature matrices...
    Wrote: ./1029_0W2.sbs_features.csv
    Wrote: ./1029_0W2.indel_features.csv
    Wrote: ./1029_0W2.cn_features.csv
  Writing signature exposures...
    Wrote: ./1029_0W2.signature_exposures.csv
  Writing classification results...
    Wrote: ./1029_0W2.classification.csv

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