I am currently working with MEGAN analyzing some metagenomic data.
First I performed BLASTX with diamond v8 and it generated files in .daa format. For taxonomic assignment I am currently working with MEGAN, but since I downloaded the latests version 6.7.1 I am getting the following error:
line 1: input ‘Taxonomy’ does not match any of legal tokens: EGGNOG INTERPRO2GO KEGG SEED
Error: Execute failed: java.io.IOException: line 1: input ‘Taxonomy’ does not match any of legal tokens: EGGNOG INTERPRO2GO KEGG SEED.
I am using databases prot_acc2tax-Nov2016.abin and prot_gi2tax-Aug2016X.bin downloaded directly from the MEGAN website.
Not only that, but when I am trying to upload the taxonomy file into the Meganizer window, the taxonomy window dissapears every time I close it, and I need to restar MEGAN for generating again. I downloaded the latest version of Java and JRE but I don’t understand what this error means.
Since I download the new version of Megan6 v6.7.3 " built 10 Mar 2017" for OSX, there is a bug concerning taxonomy tree. My Data (from a CSV file with virus taxo and counts) seems to be download but then, when I want to change the rank to create a tree, nothing happens, I can not do something except kill the app Megan6.
I have used same data file with the last version of Megan6 or Megan5 and It was okay.
could you give me more details. I have tried opening CSV files that I have and that appears to work without a problem, perhaps give me a screen shot that shows the problem, or what do you see in the Log Window?
This screen shot is after a kingdom rank request: first, the tree is not correct (my data contains only virus) and finally, the app doesn’t response anymore if I request modifications of rank (I have to kill the app). It is the same kind of bug with any ranks (family, genus, speces…)
I have tried the v6.7.4 and it still doesn’t work.
The reason why CSV import is failing is that MEGAN can’t parse taxon names that are prefixed with taxonomic rank indicators such as d__, f__ etc.
So, a quick fix is to simply replace all underscores in your file by spaces (including those inside names) and the file then can be imported.
Thank you, I replaced all __ or _ by a space in all data (including inside names) and it still doesn’t work. (I also removed rank indicators to test and it’s the same problem.) Even if I remove “|” it is the same thing.
By the way, I tried with v5.11.3 and all files worked perfectly (with __ or without)
Do you have any suggestions or idea to fix my problem?