Question: how to recover the interrupted RAXML run
0
gravatar for victoria_aleks
2.1 years ago by
victoria_aleks30 wrote:

Dear all, my RAXML run was interrupted after all bootstraps were completed. The RAXML specialists advice: "However, since you already have the bootstraps, you can now independently compute a couple of ML trees (see manual) and then use these results to do post-analyses ..." (https://groups.google.com/forum/?hl=en#!searchin/raxml/interrupted$20run%7Csort:date/raxml/BoFLQYrBlT8/pqLRqIgWxVYJ)

Unfortunately I cannot find the needed command in the manual. Can anybody, please, point me the right place or explain how to build the best-scoring ML tree and continue with the analysis if the raxml bootstrap file has been generated already?

thank you for the help in advance! :)

raxml phylogeny • 972 views
ADD COMMENTlink modified 23 months ago by h.mon30k • written 2.1 years ago by victoria_aleks30
0
gravatar for h.mon
23 months ago by
h.mon30k
Brazil
h.mon30k wrote:

By default, RAxML doesn't perform bootstraps. If you already have the bootstraps but didn't perform the ML searches for best tree, first run RAxML with -f d(whichis the default) or -f o (slower, but slightly more accurate likelihood scores), then use -f b to draw bootstraps onto the best tree.

So for example, to perform 100 searches for best trees, each search starting from a different random tree:

raxmlHPC ­-f d ­-m GTRCAT ­-p 12345 ­-s alg ­-n MLTrees -N 100

Then, to add the bootstraps to the best tree:

raxmlHPC ­-f b ­-t bestTree ­-z bootstrapTrees ­-m GTRCAT ­-n best+boot

Make sure to pass different random number seeds to RAxML and not
only 12345 as I have done in the examples.

ADD COMMENTlink written 23 months ago by h.mon30k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1029 users visited in the last hour