goseq error 'names' attribute [1] must be the same length as the vector

Hi, I am having following goseq error while using two inputs shown below:


As a genome file I used both gtf and fasta files of the potato genome but the error message has not changed (the file format was not indicated in the tutorial).

How should I proceed?

Hi @aaak,

this history reproduces the analysis in which you have faced difficulties: history goseq. I suggest you have a look at it, probably you will find the cause of the problem. If you cannot find the problem, please share your history with me.


@galladoalba I could not find what the problem is. I tried the analysis on eu server as you shared; however, no idea about why I am having this problem. One more thing, you said :

what do you mean with that? Does the analysis in EU server affects analysis in AU server?

I am leaving the link in case that you want to see the history of the analysis :


Thanks, I’ll check it.

Hi @aaak,
the problem is that Limma goseq requires inputs ( differentially expressed genes file and gene lengths file) of the same number of entries; in order to fix the problem, you need to run Limma without filtering low expressed genes.


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Now, I understand in my length file I have more than 30000 genes whilst only about 25000 genes are available… I will run the analysis again with equal number of genes, I will let you know if it works… heartfelt thanks.

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Nope… it did not work out.

Could you share your history with me again, please?

To help you understand my doings, let me explain how I proceeded.

I merged all data files as you can see in 11. and I created status and length files by cutting necessary columns. Then I ran the goseq

the result was the same error message. The link is below.


Hi @aaak,
in that case the problem is that the gene annotation file should have this format: annotation file.
This paper provides some information about how to obtain the GAF (Go Annotation File) corresponding to S. tuberosum.


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Heartfelt thanks for all your help