vcontact2 failure when no cluster found

Issue #40 new
Former user created an issue

vcontact2 failure when no cluster found, see

[mcl] jury pruning marks: <100,100,100>, out of 100
[mcl] jury pruning synopsis: <100.0 or really really really good> (cf -scheme, -do log)
[mcl] output is in vConTACT2_Results/merged.self-diamond.tab_mcl20.clusters
[mcl] 0 clusters found
[mcl] output is in vConTACT2_Results/merged.self-diamond.tab_mcl20.clusters

Please cite:
    Stijn van Dongen, Graph Clustering by Flow Simulation.  PhD thesis,
    University of Utrecht, May 2000.
       (  http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
       or  http://micans.org/mcl/lit/svdthesis.pdf.gz)
OR
    Stijn van Dongen, A cluster algorithm for graphs. Technical
    Report INS-R0010, National Research Institute for Mathematics
    and Computer Science in the Netherlands, Amsterdam, May 2000.
       (  http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
       or  http://micans.org/mcl/lit/INS-R0010.ps.Z)

INFO:vcontact2: Building the cluster and profiles (this may take some time...)
If it fails, try re-running using --blast-fp flag and specifiying merged.self-diamond.tab (or merged.self-blastp.tab)

============================This is vConTACT2 0.9.19============================



----------------------------------Pre-Analysis----------------------------------


------------------------------Reference databases-------------------------------


-------------------------------Protein clustering-------------------------------
Traceback (most recent call last):
  File "/opt/gensoft/exe/vcontact2/0.9.19/bin/vcontact2", line 4, in <module>
    __import__('pkg_resources').run_script('vcontact2==0.9.19', 'vcontact2')
  File "/opt/gensoft/exe/vcontact2/0.9.19/venv/lib/python3.8/site-packages/pkg_resources/__init__.py", line 667, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/opt/gensoft/exe/vcontact2/0.9.19/venv/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1471, in run_script
    exec(script_code, namespace, namespace)
  File "/opt/gensoft/exe/vcontact2/0.9.19/venv/lib/python3.8/site-packages/vcontact2-0.9.19-py3.8.egg/EGG-INFO/scripts/vcontact2", line 757, in <module>
  File "/opt/gensoft/exe/vcontact2/0.9.19/venv/lib/python3.8/site-packages/vcontact2-0.9.19-py3.8.egg/EGG-INFO/scripts/vcontact2", line 469, in main
  File "/opt/gensoft/exe/vcontact2/0.9.19/venv/lib/python3.8/site-packages/vcontact2-0.9.19-py3.8.egg/vcontact2/protein_clusters.py", line 187, in build_clusters
  File "/opt/gensoft/exe/vcontact2/0.9.19/venv/lib/python3.8/site-packages/vcontact2-0.9.19-py3.8.egg/vcontact2/protein_clusters.py", line 252, in load_mcl_clusters
OverflowError: cannot convert float infinity to integer

dur to log10(0) -> regardds

Eric

Comments (1)

  1. Ben Bolduc

    Hi Eric,

    Thanks for bringing up this issue. Did you run your dataset with a reference database, and how many genomes were used?

    Unless there are no references, this shouldn’t occur unless your input genomes have no relationships to each other, or they consist of fewer than 3 genes each.

    -Ben

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