Entering edit mode
8.7 years ago
heshamgibriel
▴
20
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?
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"?
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?