Interruption at cluster step

[sainadfensi]

Hi Marek, Thanks for the development and maintenance of SVclone.

I've tried filtering with and without having CNV input, and both get the same error when running the following cluster step.

code: svclone cluster -s $sample --snvs $out -cfg $config -o Output/$sample printout:

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Missing column: subclonal_cn1. Set subclonal_cn as frac_cn1_sub1 < 1
Missing column: subclonal_cn2
                    Set subclonal_cn as frac_cn2_sub1 < 1
Running VB-Normal-Binomial on a 45-by-1 data with 1 clusters ...
Converged in 362 steps.
Running VB-Normal-Binomial on a 45-by-1 data with 3 clusters ...
(... I removed similar messages about converging ..)

Converged in 891 steps.
null device
          1
Traceback (most recent call last):
  File "/usr/local/python/3.6.5/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2898, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 1675, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1683, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'ref'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/scratch/RDS-FMH-PopPCaGenomics-RW/Jue/Tools/SVclone/sv_clone-env/bin/svclone", line 8, in <module>
    sys.exit(main())
  File "/scratch/RDS-FMH-PopPCaGenomics-RW/Jue/Tools/SVclone/sv_clone-env/lib/python3.6/site-packages/SVclone/cli.py", line 187, in main
    args.func(args)
  File "/scratch/RDS-FMH-PopPCaGenomics-RW/Jue/Tools/SVclone/sv_clone-env/lib/python3.6/site-packages/SVclone/run_clus.py", line 209, in run_clustering
    format_snvs_for_ccube(snv_df, sample_params, cluster_params, cc_file)
  File "/scratch/RDS-FMH-PopPCaGenomics-RW/Jue/Tools/SVclone/sv_clone-env/lib/python3.6/site-packages/SVclone/run_clus.py", line 77, in format_snvs_for_ccube
    sup, dep, Nvar, norm_cn = load_data.get_snv_vals(df, cparams)
  File "/scratch/RDS-FMH-PopPCaGenomics-RW/Jue/Tools/SVclone/sv_clone-env/lib/python3.6/site-packages/SVclone/load_data.py", line 34, in get_snv_vals
    n = df['ref'].map(float).values
  File "/usr/local/python/3.6.5/lib/python3.6/site-packages/pandas/core/frame.py", line 2906, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/usr/local/python/3.6.5/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2900, in get_loc
    raise KeyError(key) from err
KeyError: 'ref'  

However, there are outputs in ccube_out/ folder:

├── sample_assignment_probability_table.txt ├── sample_ccube_sv_results.pdf ├── sample_ccube_sv_results.RData ├── sample_cluster_certainty.txt ├── sample_multiplicity.txt └── sample_subclonal_structure.txt

All the SVs clustered to a single cluster shown in sample_assignment_probability_table.txt.

[mcmero]

This means your input SNVs file doesn't have a ref column (reference counts). Can you post a sample of your $out file?.

[sainadfensi]

Hi Marek,

Thank you for the prompt response and sorry for my late reply. It turned out I was doing wrong for using the output file of the previous filtering step instead of using a VCF file for the --snvs flag. All the steps are processed smoothly.

Can you help me quick check the result of two example running (./run_example.sh, ./run_example_wsnvs.sh). I only see one cluster for the two examples. Is that correct?

[mcmero]

You should get one cluster for the SV results, and two clusters for the SNV results.

[sainadfensi]

Oh right, there are two clusters for SNVs. Thanks!