search

ariloytynoja / prank-msa

Automatically exported from code.google.com/p/prank-msa
25 stars 6 forks source link

conon alignment giving likelihood = 0 error #19

Open szimmerman92 opened 4 years ago

szimmerman92 commented 4 years ago

Hi,

I am using PRANK v.170427.

I am having trouble with codon alignment. When I execute the line of code prank -d=OG0017868.ffn -o=prank_test_out -F -codon

I get the following errors

Generating multiple alignment: iteration 1. ERROR!!! !!! Unexpected likelihood == 0. ERROR!!! !!! Looking at each site: Site 1 log likelihood = -4.110874 Site 2 log likelihood = -10.329994 Site 3 log likelihood = -24.984849 ... Site 325 log likelihood = -4.110874 Site 326 log likelihood = -4.110874 Site 327 log likelihood = -4.110874 ERROR!!! !!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences).

This happens for every multiple alignment iteration. I am only using 4 sequences. When I run the code without performing codon alignment, it works perfectly.

Do you know what might be wrong? Attached you can find my fasta file. The suffix was originally .ffn but I changed it to .txt so I could attach here.

OG0017868.txt

.

Thank you.

wshropshire commented 4 years ago

I'm having the same issue with the same error. I saw an older issue brought up, but the resolution was using a new version, i.e. v1.70427 #12

szimmerman92 commented 4 years ago

Thanks for the response. I will try using the latest version. Since I posted this I have also started to use CANOPY instead since, according to the publication, it seems like a more robust aligner compared to PRANK and it seems to work well.

wshropshire commented 4 years ago

Found a (hopeful) solution. The development branch version of prank (prank-170703) does not throw this error. I'm assuming the conda recipe package which lists 170427-1 and 170427-2 uses one of these development branch versions that are not the stable version. Anyways, this should solve future problems hopefully!

vicenciooostra commented 3 years ago

Anyone still reading this? :-)

I have the same problem, prank v.170427. Where can I find this newer version?

Kind regards, Vicencio

szimmerman92 commented 3 years ago

You can find it on the wasabi website: http://wasabiapp.org/download/prank/development/

Installation instructions can be found at this link. http://wasabiapp.org/software/prank/prank_installation/

vicenciooostra commented 3 years ago

Hi - many thanks for the link! That solved my issue.

Kind regards, -v

dynamiskduo commented 3 years ago

Hi :) I found that the issue in my case could be solved by removing stop codons (PRANK v.170427). Maybe that is helpful for others? Kind regards, Amanda