Prokka tool error with dataset




I have just run a Prokka analysis using SPAdes_contigs.fasta data and the analysis ran for about 24hrs before it failed with the error :

" tool error An error occurred with this dataset: Failed to find or download one or more job outputs from remote server "

Bit confused about this.

Thank you,



Hi Marco - This looks like a transient cluster error message. Please try a rerun and let us know if the job errors again. If it does, we can troubleshoot more from there.



Hello Jennaj,

Thank you for the quick reply. I reran the same job on Galaxy Australia and Europe. Galaxy Australia returned the same error while Galaxy Europe returned the error:

“Fatal error: Exit code 2 ()
[06:15:49] Please rename your contigs OR try ‘–centre X --compliant’ to generate clean contig names.”

thank you very much,



Check the contig/chromosome names in your inputs. You may need to run the tool NormalizeFasta to remove description line content from the fasta input.

All Support FAQs:


great, thank you! fingers crossed that helps.

One other question. Is it possible to bin my contigs using Galaxy? I cant seem to find some of the binning programs I am familiar with such as MetaBAT, MaxBin, or ESOM on the Galaxy platform.

Thank you very much!,



MaxBin2 is currently wrapped for Galaxy and available in the ToolShed for use in your own local Galaxy. It is not installed at the usegalaxy.* public Galaxy servers.

The Mothur tool suite also has binning/clustering tools. These can be found in the ToolShed and also at the usegalaxy.* servers, including Galaxy Main These tutorials include Mothur tools:

More metagenomics tools can be found in the ToolShed and at public Galaxy servers, usually under a tool section named like “Metagenomics”. Those with a metagenomics domain-focus are listed here: