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Having trouble running my nexus in Cippress Portal (Read 437 times)
Dec 9th, 2019 at 7:59am

KIM   Offline
YaBB Newbies

Posts: 2
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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
 
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Reply #1 - Dec 9th, 2019 at 4:53pm

Olga Golosova   Offline
YaBB Administrator

Posts: 326
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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!
 
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Reply #2 - Dec 10th, 2019 at 4:04am

KIM   Offline
YaBB Newbies

Posts: 2
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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'
 
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Reply #3 - Dec 10th, 2019 at 11:54am

Olga Golosova   Offline
YaBB Administrator

Posts: 326
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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...
 
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Reply #4 - Feb 6th, 2020 at 6:50pm

Olga Golosova   Offline
YaBB Administrator

Posts: 326
*****
 
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'
 
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