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https://forum.ugene.net/forum/YaBB.pl General Category >> Bugs and Issues >> Having trouble running my nexus in Cippress Portal https://forum.ugene.net/forum/YaBB.pl?num=1575853177 Message started by KIM on Dec 9^th, 2019 at 7:59am

Title: Having trouble running my nexus in Cippress Portal
Post by KIM on Dec 9^th, 2019 at 7:59am

I am getting this error,

Unrecognized DNA/RNA character '_'
   Error while reading character position 1 (charCode -1)
   Deleting previously defined characters
   Deleting previously defined taxa
   Error when setting parameter "MatrixInfo" (2)
   There was an error on at least one processor
   The error occurred when reading char. 16-23 on line 202
      in the file 'infile.nex'

Returning execution to command line ...

Error in command "Execute"

MrBayes >
Quitting program
I will attach my nexus. Any help would be greatly appreciated

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=alignment_with_outgroupCrenuch_4loci_help_nex.txt (190 KB | 426 )

Title: Re: Having trouble running my nexus in Cippress Portal
Post by Olga Golosova on Dec 9^th, 2019 at 4:53pm

The problem is that some sequences contain " " (space characters) in their names. This is not treated well in the current UGENE version. For now, please avoid such names and replace " " by "_" or another character. See the attached file.

We're going to fix the issue in the future UGENE versions.

Thanks for your feedback!

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=corrected_alignment_with_outgroupCrenuch_4loci_help.nex (190 KB | 477 )

Title: Re: Having trouble running my nexus in Cippress Portal
Post by KIM on Dec 10^th, 2019 at 4:04am

I fixed all the spaces and still got this error.....

Unrecognized DNA/RNA character '_'
   Error while reading character position 1 (charCode -1)
   Deleting previously defined characters
   Deleting previously defined taxa
   Error when setting parameter "MatrixInfo" (2)
   There was an error on at least one processor
   The error occurred when reading char. 16-23 on line 202
      in the file 'infile.nex'

Title: Re: Having trouble running my nexus in Cippress Portal
Post by Olga Golosova on Dec 10^th, 2019 at 11:54am

See the attached file in my previous post. Please try to compare it with your original file and with the new one. Possibly, some space characters are still left...

Title: Re: Having trouble running my nexus in Cippress Portal
Post by Olga Golosova on Feb 6^th, 2020 at 6:50pm

Hello.

We're investigating the issue you reported and found out that it wouldn't be so easy to fix it. It is not clear enough from the file whether the space character belongs to a sequence name or it separates a sequence and its name.

Where did you get the Nexus file from your example? Was it produced by some software or downloaded from a database?

In general, you should actually enclose a sequence name with space character into single quotes like that (see the space character before "_sp..."):

Quote:

'Elachocharax _sp_4696'

Title: Re: Having trouble running my nexus in Cippress Portal
Post by Benny on Nov 24^th, 2020 at 2:13pm

wrote on Apr 1^st, 2469 at 2:07am:

Please try to compare it with your original file and with the new one. Possibly, some space characters are still left...