Question: (Closed) error in json to flatfile.pl prpgram running in jbrowse.
1
gravatar for rajesh
3.8 years ago by
rajesh 60
India/Chandigarh/
rajesh 60 wrote:

i am working with JBrowse for genome alignment. When i upload gff3 file and run following command it give error which i am listing here. can anybody suggest me how to deal with that error.

rajesh:~/Desktop/JBrowse-1.12.0$ perl bin/flatfile-to-json.pl --out sample_data/json/try/ --gff sample_data/raw/try/xx.gff3 --key mRNA --type mRNA --trackLabel mRNA --className feature5

error are:

GFF3 parse error: some features reference other features that do not exist in the file (or in the same '###' scope).  A list of them:
 ID                 |           Cannot Find
----------------------------------------------------------------------
ENST00000473466     | Parent=ENSG00000097021
ADD COMMENTlink modified 3.8 years ago by Vitis2.4k • written 3.8 years ago by rajesh 60

Hello rajesh !

We believe that this post does not fit the main topic of this site.

OP does not respond to posts after asking questions. Question closed until OP responds.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.8 years ago by RamRS30k
1
gravatar for Vitis
3.8 years ago by
Vitis2.4k
New York
Vitis2.4k wrote:

It is exactly what the error message says: the feature ENST00000473466 has a parent feature ENSG00000097021, and ENSG00000097021 is not in your GFF3.

ADD COMMENTlink written 3.8 years ago by Vitis2.4k
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