Hi Eilyn!
I have the same problem, Was it fixed? If so, can you share?
Regards,
Henry
1 Like
Welcome, @SudoSchrodinger
Let’s move this over to a new topic since whatever was going wrong for that prior Q&A wasn’t clarified here. There are a few things that can go wrong. Try reviewing the resources below to get oriented, then post back your details if you need more help → How to get faster help with your question
Xref
- Galaxy Training! Tutorials that include FEELnc (has example data/usage)
- FAQ: Working with GFF GFT GTF2 GFF3 reference annotation
- Good overview of reference data content, any analysis → FAQ: Extended Help for Differential Expression Analysis Tools
Hi, I am also getting error while running FEELnc. Getting this error every time. Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Filtered transcripts will be available in file: ‘out_feelnc/filter/candidate_lncRNA.filter.log’
Parsing file ‘dataset_833f0a7b-9577-46ea-b9c3-d4336323d6b6.dat’…
please suggest me some solutions to it
Welcome, @poora
Thanks for sharing your error message! The comments so far just look like processing log chatter, without any clues about what might be going wrong yet.
See the first reply here – checking the full job logs, then checking your reference data is usually where to start with for this tool. Then proceed to check the other inputs, and maybe compare your usage to the tutorial.
If you want to share more details, we can help you to review this closer. See the banner at this forum, also quoted below, for the kind of information we need for troubleshooting and where to find that in the application.
I’ll watch for your reply, thanks! 
Parser::parseGTF => Data Structure returns an empty hash
Possible reasons:
*Feature level ‘exon,CDS,stop_codon,start_codon’ is not present in 3rd field of ‘out_feelnc/filter/candidate_lncRNA.filter.gtf’
*chromosome/seqname (chr) or patch chromosome…
*Filtering tag/Attributes (–filter|-f) option returns no results
Try --help for help
Error: Cannot read your input lncRNA GTF file ‘out_feelnc/codpot//candidate_lncRNA.codpot.lncRNA.gtf’…
For help, see:
FEELnc_classifier.pl --help
Usage:
FEELnc_classifier.pl -i lncRNA.gtf -a mRNA.gtf > lncRNA_classes.txt
cat: can’t open ‘out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt’: No such file or directory
cat: can’t open ‘out_feelnc/classifier/candidate_lncRNA.classifier.log’: No such file or directory
Every time I got this error. I used hg38 reference genome and annotation file. Can you suggest me which type of annotation and reference genome i should use to avoid the error.
Hi @poora
This seems to be reporting a problem with the GTF file that you are using.
Specifically, the tool is looking for features labeled as exon in the 3rd field of the GTF file but didn’t find them. You might need to simply the format of the file you have, or you may need to source a different reference annotation file.
This guide explains how to source human reference data. → Reference genomes at public Galaxy servers: GRCh38/hg38 example
Please let us know if that helps or not.