AssertionError: More than 1 node for blast in config XML

[taoqxtaozi]

Hi,

I'm running with cactus-bin-2.1.1, I notice that you mention "A non-default configuration (included in the dataset) was used to change the alignment filtering in both runs to better support the high degree of polytomy in the star-tree runs." in your paper, so I download the star_config.xml from http://courtyard.gi.ucsc.edu/~jcarmstr/datastore/progressiveCactus.EvolverSim.CactusInput.EvenlySpread.tar.gz. error1.txt and try to run star tree as a guide tree with it. Here is my command:

cactus --realTimeLogging --defaultMemory 20G --maxCores 30 --maxMemory 180G --configFile ./star_config.xml ./jobstorecluster4 ./aln.txt ./aln_startree_noref_starconfig.hal

and my aln.txt is:

(Monkey,Human,Bonobo,Chimp)ance;
Monkey ./Monkey.fa
Bonobo ./Bonobo.fa
Chimp ./Chimp.fa
Human ./Human.fa

And I get the error:

File "/picb/phylcomb/taoqixin/software/cactus-bin-v2.1.1/cactus_env/lib/python3.8/site-packages/cactus/shared/common.py", line 120, in findRequiredNode
        assert len(nodes) == 1, "More than 1 node for %s in config XML" % nodeName
    AssertionError: More than 1 node for blast in config XML

the complete message is in the attachment. When I run star tree as a guide tree with the default configuration, there is no problem. Would it because of the version of cactus?

[taoqxtaozi]

Looking forwarding to your reply, thanks a lot!

[glennhickey]

The config.xml format often changes between Cactus versions. So unless you are using a config.xml that is derived from the version of Cactus you are using, then there is not guarantee that it works. This is almost certainly the issue here.

If you want the best performance, use the latest version of Cactus with its default configuration.

[taoqxtaozi]

Ok, thanks!