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  • dmacmillan
    Member
    • Jan 2012
    • 49
    #1

    Oases Help

    I get an error when trying to do the final merge stage of oases. This is my command and output:

    ../assemblers/oases_0.2.07_x11/oases MergedAssembly/ -merge yes

    [0.000000] Reading graph file MergedAssembly//Graph2
    [0.023690] Graph has 2355595 nodes and 5929364 sequences
    [1282.942385] Reading read set file MergedAssembly//Sequences;
    [1293.465792] 5929364 sequences found
    [1327.296416] Done
    [1389.423138] Removing contigs with coverage < 3.000000...
    [1389.502600] Concatenation...
    [1389.918961] Renumbering nodes
    [1389.918980] Initial node count 2355595
    [1389.923377] Removed 0 null nodes
    [1389.923396] Concatenation over!
    [1389.923399] Clipping short tips off graph, drastic
    [1389.970080] Concatenation...
    [1390.386237] Renumbering nodes
    [1390.386257] Initial node count 2355595
    [1390.390656] Removed 0 null nodes
    [1390.390673] Concatenation over!
    [1390.390675] 2355595 nodes left
    [1390.390683] Correcting graph with cutoff 0.200000
    [1390.390691] Removing low coverage edges from the graph
    Segmentation fault

    Has anyone experienced anything such as this? If so do you have any ideas as to how I can get around it?
    Last edited by dmacmillan; 07-03-2012, 09:01 AM.
    Tags: oases velvet
  • robertorun
    Member
    • Nov 2009
    • 22
    #2
    I also met the same errors.
    I only downloaded the lastest velvet and oases , then recompile them , now ,they are work smoothly!

    Comment

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