Comments (4)
Check the contents of run/h99_longest_transcript/lifted_cleanup.log
maybe
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.
Related Issues (20)
- faToTwoBit: cannot execute binary file HOT 5
- gt gff3 error HOT 7
- liftover gtf file HOT 1
- Present as a set of scripts
- gt gff3: error: Parent ... was not defined (via "ID=") HOT 6
- mitochondrial genes HOT 3
- flo compilation error HOT 1
- Workflow manager? HOT 1
- Flo failed at the GenomTools section HOT 3
- flo failed on Large genome HOT 9
- file "-" does not contain 9 tab (\t) separated fields HOT 7
- Syntax issue with rake HOT 2
- Error when blat begins HOT 5
- undefined method `last' for nil:NilClass (NoMethodError)
- Expecting number line ERROR HOT 2
- cc command not found HOT 1
- GFF format issue with CoGe input
- install.sh fails with a make error for libgenometoools.so HOT 2
- Issue a release & publish on Bioconda? HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from flo.