Parseval error: can not continue running to compare two files together

Question

[heshamgibriel]

Hi all!

I am facing quite a strange problem when using parseval to compare gene models. Initially, I installed parseval, run it and got the output and it worked perfectly. However, recently I was trying to do the same thing, to compare two gff files (old and new), but I get this strange error message:

warning: seqid "21" on line 2 in file "file name" has not been previously introduced with a "##sequence-region" line, create such a line automatically
[ParsEval] error: Parent "ID name" on line 240 in file "file name" was not defined (via "ID=")

This is the command that I used:

parseval -o -f html old file.gff3 new file.gff3

In order to be sure that the problem I am facing is not the due to file errors, I download other gff files and tried to compare them. However, I still get the same error message.

Does this problem have to do with parseval or my files or what exactly?

[Juke34]

Hi,

The problem seems to come from the gff file. Could you grep "ID name" in your file and looks if you find any line that contains Parent="ID name"?

[heshamgibriel]

But I still don't understand why when I compare two similar files together from different databases I get the same error?

Also, it's quite weird that when I ran parseval previously on those files, I did not get any error at all. Now, I see these error messages whenever I want to run parseval?