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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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error with mutifurcation #1516

Closed matdechiara closed 2 weeks ago

matdechiara commented 2 weeks ago

Hi, I need to align genomes for which I do not have a tree ( I am doing the algnment to be able to extract snps and create one ). I used a fake tree, just listing all the assemblies in order, which wa working with previous version of cactus and the results were quite reliable for the organisms I work with.

Now I get this error: Such nodes have been shown to drastically drop coverage in recent versions of Cactus. For best results, binarize your tree and try again. You can override this check by toggling "allow_multifurcations" to "1" in the configuration XML

I actually found this file : cactus/src/cactus/cactus_progressive_config.xml and I modified it here

                    default_internal_node_prefix="Anc"
                    default_branch_len="1"
                    default_branch_len_pangenome="0.025"
                    allow_multifurcations="1"

I still get the same error message though. What could be the problem?

Thanks

matdechiara commented 2 weeks ago

Sorry, I did not realised I had to force cactus to re-read the config file with the command --configFile