ValueError: The condensed distance matrix must contain only finite values

[stefano...@gmail.com]

Hi Andy,

I'm runnning PyClone in a conda environment in this way:

PyClone run_analysis_pipeline \

--in_files \

sample1_all_muts.tsv \

sample2_all_muts.tsv \

sample3_all_muts.tsv \

--tumour_content 0.9 0.9 0.9 \

--sample 1 2 3 \

--burnin 10000 \

--prior total_copy_number

After completing the iterations (printed as std out), PyClone stops with the following error:

Traceback (most recent call last):

  File "/scheloni/local/src/miniconda3/envs/pyclone/bin/PyClone", line 337, in <module>

    main()

  File "/scheloni/local/src/miniconda3/envs/pyclone/bin/PyClone", line 78, in main

    args.func(args)

  File "/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/pyclone/run.py", line 53, in run_analysis_pipeline

    args.thin

  File "/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/pyclone/run.py", line 308, in _build_table

    mesh_size=mesh_size

  File "/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/pyclone/post_process/clusters.py", line 46, in load_summary_table

    thin=thin,

  File "/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/pyclone/post_process/clusters.py", line 95, in load_table

    labels = cluster_pyclone_trace(config_file, burnin, thin)

  File "/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/pyclone/post_process/clusters.py", line 29, in cluster_pyclone_trace

    labels = cluster_with_mpear(X)

  File "/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/pydp/cluster.py", line 25, in cluster_with_mpear

    Z = average(dist_mat)

  File "/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 323, in average

    return linkage(y, method='average', metric='euclidean')

  File "/mnt/PGP/homes/scheloni/local/src/miniconda3/envs/pyclone/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 713, in linkage

    raise ValueError("The condensed distance matrix must contain only "

ValueError: The condensed distance matrix must contain only finite values.

Could you suggest me which values are taken and processed from the input files to fill the condensed distance matrix?
Do you think that something could be wrong with the input or maybe the error could be due to something else? 
I would be happy to share any tsv, config, yaml or trace files if necessary.

For your information, I'm running PyClone-0.13.0 installed through conda install pyclone -c aroth85 as you suggested in the manual. All the dependencies and packages versions needed are satisfied.


Thank you in advance for you precious suggestions,
Stefano

[Andrew]

Hi Stefano,

The error is from another library, scipy, not PyClone. The likely reason is that something went wrong in the PyClone run. It is hard to know what without the input files and results.

Best wishes,

Andy