Question: (Closed) Fatal Errors occurring with htseq analysis
gravatar for encarnaciona
8 months ago by
encarnaciona20 wrote:


I am in the process of analyzing some RNAseq data. I uploaded the data and successfully mapped the sequences to the the C. elegans genome using the HISAT2 program. Currently I am trying to convert my map reads to gene counts using the htseq-count program but keep encountering a fatal error: Fatal error: Unknown error occured Error occured when processing GFF file (line 4 of file /galaxy-repl/main/files/024/011/dataset_24011093.dat): Failure parsing GFF attribute line [Exception type: ValueError, raised in]

Is there a way to bypass this or keep it from happening?

Thank you so much,


ADD COMMENTlink written 8 months ago by encarnaciona20

Hello encarnaciona!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

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


ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k


I'm trying to find errors similar to mine, and I'm not seeing a way to fix this. I've tried converting the genome to a GTF file, but I'm still getting the same errors.

ADD REPLYlink written 8 months ago by encarnaciona20

Did you check the formatting help here?

And see the post here:

There are others in the >> side bar based on keyword matches or you can do a search. This question comes up when there is a format problem with the annotation. Fixing the GTF how to move forward.

I am not sure what you mean by "I've tried converting the genome to a GTF file". The gene_id and transcript_id attributes should be included in the GTF for this tool, along with the other proper formatting, including the datatype assignment. You may need to obtain a GTF from a pubic source. iGenomes is one good choice. All is covered in the links given in the prior Q&A.

All support FAQs are here:

And Galaxy tutorials that include htseq_count/RNA-seq analysis are here:

If the format/content/datatype is a match and your usage aligns with that in the tutorials (please check first, as correcting those items will be the first steps in any troubleshooting we help with), a bug report can be sent in for more review/feedback if working at Galaxy main https://usegalaxy.orgthere and or can reproduce the error there. Please include a link to this post in the bug report comments.

ADD REPLYlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k
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