goseq error with importing category file

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1

I am trying to run goseq on an RNA-seq dataset from A. thaliana. I need to import a GO category file, and I have tried with two different files, but it keeps failing.
Most recently I downloaded the GO file from TAIR functional annotation data but it is still giving me the following error:
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.6 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /usr/local/tools/_conda/envs/mulled-v1-ac9928cd0c80e707f8c859eeebc088f04f34d841be6e3b5ac8f7a331c

Here is the link to my history with the files I used, two different GO files and the failed jobs if anyone can help- Galaxy

Thanks!

2

Hi @jbliss
check examples of expected input files at the bottom of goseq job setup page. All files have two columns and no header. Maybe consider adjusting your files to the expected format using tools in Text Manipulation section (remove first lines, cut columns). Maybe convert GZipped file with GO categories into plain text tabular by clicking at Edit Attributes (pencil icon) > Convert tab in the middle window) > Select an appropriate option in pull-down menu.
Hope that helps.
Kind regards,
Igor

3

Hello @jbliss Were you able to solve the problem? I am countering the same issue.