gff_recover error about flo HOT 4 OPEN

Check the contents of run/h99_longest_transcript/lifted_cleanup.logmaybe

from flo.

(and let me know too)

from flo.

I'm reasonably sure at this point that this is a problem with the gff I am using, specifically the feature IDs in the 3rd column. If I can come up with a suggestion for some error handling, I'll go ahead and post it. Otherwise, this is probably a idiosyncratic problem on my side rather than something to handle in the software itself.

from flo.

Hi; I have the same problem than @cmatKhan just show in his picture.
I would like to know how we can fix the problems. This is last lines of the run/Longest_Transcript/lifted_cleanup.log :

Chr1	kh2012	three_prime_UTR	5073729	5073960	.	+	.	Parent=KH2012:KH.C1.8.v5.A.ND1-1;Target=KH.C1.8.v5.A.ND1-1 900 1131
Chr1	kh2012	three_prime_UTR	2551018	2551052	.	+	.	Parent=KH2012:KH.C1.5.v2.A.ND1-1;Target=KH.C1.5.v2.A.ND1-1 4516 4550
Chr1	kh2012	three_prime_UTR	2551316	2551581	.	+	.	Parent=KH2012:KH.C1.5.v2.A.ND1-1;Target=KH.C1.5.v2.A.ND1-1 4551 4807
Chr1	kh2012	three_prime_UTR	5670475	5670962	.	+	.	Parent=KH2012:KH.C1.1056.v1.A.ND1-1;Target=KH.C1.1056.v1.A.ND1-1 1631 2118
warning: line 1 in file "-" does not begin with "##gff-version" or "##gvf-version", create "##gff-version 3" line automatically
gt gff3: error: Parent "KH2012:KH.C1.976" on line 1 in file "-" was not defined (via "ID=")

Any idea or hint for how to correct this ?

I'm using the gff file attached with this message.

I trying to watch RakeFile and gff_recover.rb but didn't see any problem, or hint for solutions...
Longest_Transcript.txt

from flo.