Question: (Closed) Fatal Errors occurring with htseq analysis
gravatar for encarnaciona
12 days ago by
encarnaciona0 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 12 days ago by encarnaciona0

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 12 days ago by Jennifer Hillman Jackson24k


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 12 days ago by encarnaciona0

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 12 days ago • written 12 days ago by Jennifer Hillman Jackson24k
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