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,


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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,


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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!,


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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:

Hello Marcos,
I had the same problem. How you resolve it?