MITOS2 error can't run job

usegalaxy.org support
,
1

Hi, I’ve tried to use MITOS2 tool, and the following error seems to persist:

The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below.

{
    "history_id": "bbd44e69cb8906b56889ef2a85e9e624",
    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mitos2/mitos2/2.1.9+galaxy0",
    "tool_version": "2.1.9+galaxy0",
    "inputs": {
        "input": {
            "batch": false,
            "product": false,
            "values": [
                {
                    "id": "f9cad7b01a47213579248114c83b5654",
                    "src": "hda",
                    "map_over_type": null
                }
            ]
        },
        "code": "2",
        "refseqver": "refseq63m",
        "linear": false,
        "addoutputs": "bed",
        "advanced|featuretypes": [
            "prot",
            "trna",
            "rrna"
        ],
        "advanced|finovl": "50",
        "advanced|best": false,
        "advanced|fragovl": "20",
        "advanced|fragfac": "10.0",
        "advanced_prot|evalue": "2.0",
        "advanced_prot|cutoff": "50",
        "advanced_prot|clipfac": "10.0",
        "advanced_prot|ncbicode": false,
        "advanced_prot|alarab": false,
        "advanced_prot|oldstst": false,
        "advanced_ncrna|locandgloc": false,
        "advanced_ncrna|ncev": "0.01",
        "advanced_ncrna|sensitive": false,
        "advanced_ncrna|maxtrnaovl": "50",
        "advanced_ncrna|maxrrnaovl": "50"
    }
}

I’ve tried several different parameters, but to no avail. Please let me know how to resolve this issue.

Many thanks!

2

Welcome @bioinfokg

Thanks for sharing the parameters! It looks like you are using the default reference index with the most current tool version. And, the topic was tagged as being for UseGalaxy.org, so that is where I am cross testing, but you can clarify if you are working somewhere else?

This is my test using the same configurations, and it ran successfully, so I think the tool and the reference index are working Ok.

My best guess is that there is some problem with your input fasta dataset. Maybe the format? You could run the data through a tool like NormalizeFasta to see if that helps. Other problems could be based on the scientific content – maybe a different reference index would be a better choice?

If that is not enough help to solve this, you are welcome to share more details and we can troubleshoot more. :slight_smile: