Parseval error: can not continue running to compare two files together
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?
• 2,027 views
•
link
updated
by
Ram
•
written
by
heshamgibriel •
•
written
by
heshamgibriel •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Extract protein sequences or names based on GFF and protein file
written by T_18 •
-
Annotation lifting to a different organism
written by Ric
-
convert Trinotate resulte to GFF file
written by Mostafa Mahmoud •
-
GFF liftOver using CrossMap is failing.
written by kirannbishwa01
-
GFF to fasta
written by mmats010 •
-
Cuffmerge: GFF Error: duplicate/invalid 'transcript'
written by pld
-
Converting gff file to gtf for htseq-count
written by natsterbug •
-
Extract flanking genes around sRNA from gff files
written by CikLa
-
check if two columns match in 2 annotation files and print those lines to a new output file
written by vineelagangalapudi •
-
use bedtools to find overlaps of bed and gff files
written by biolab
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?