Question: Clonalorigin Error "Segmentation Fault"
gravatar for thakurshalabh
7.8 years ago by
thakurshalabh60 wrote:


Im using ClonalOrigin program for inference of homologous recombination in 54 bacterial strains. I have installed the program correctly as per the instruction given on the program's website. Also I have prepared the inputs in the specified format (1) Mauve XMFA alignment format (2) Consensus clonal phylogeny estimated using Clonal Frame.

I am running the test data set with following command:

warg -a 1,1,0.1,1,1,1,1,1,0,0,0 -x 1000000 -y 1000000 -z 10000 clonaltree_names.nwk Test_input.xmfa.1 Test_input_phase.xml

But it is giving me an error saying "Segmentation fault".

I also tried changing some other options

warg -a 1,1,0.1,1,1,1,1,1,0,0,0 -i 54,8,508,500,100,50 -x 1000000 -y 1000000 -z 10000 clonaltree_names.nwk Test_input.xmfa.1 Test_input_phase.xml

Where -i takes six parameters, first one of which is number of sequences in a sample. In this case its 54 sequences, one from each strain. Other parameters were left default.

However, still the program is giving me same error saying "Segmentation fault".

Has anyone tried using ClonalOrigin and came across this error? How did you got around the error? or any suggestion. I guess this is an issue related to some memory allocation, but I don't know how to make it work. My CPU is having 24 GB RAM which I guess should be good enough for this analysis.

please let me know if some one has a solution to this.

Thank you

recombination • 1.7k views
ADD COMMENTlink written 7.8 years ago by thakurshalabh60
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